
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.85.4149/Clusters2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.85.4149/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/KIRP-TP/3536999/KIRP-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/KIRP-TP/3351306/KIRP-TP.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ALL", "-oT=", "-nV=Nozzle.R1", "-OP=AGGREGRATED_CLUSTER", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"  "-oT="
[1] "opt"                     "-OP=AGGREGRATED_CLUSTER"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  

nPatients in clinical file=104, in cluster file=127, common to both=104
[1]   8 104
[1] "CN_CNMF"
[1] 3
 1  2  3  4  5 
20 38  9 20 17 
 1  2  3  4  5 
20 38  9 20 17 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
21 40 27 
 1  2  3 
21 40 27 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3 
26 24 25 
 1  2  3 
26 24 25 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
18 36 21 
 1  2  3 
18 36 21 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3  4 
28 37 22 17 
 1  2  3  4 
28 37 22 17 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
37 29 10 28 
 1  2  3  4 
37 29 10 28 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
30 35 23 
 1  2  3 
30 35 23 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3 
37 15 36 
 1  2  3 
37 15 36 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "DAYSTOLASTKNOWNALIVE"                  
[10] "KARNOFSKYPERFORMANCESCORE"             
[11] "HISTOLOGICALTYPE"                      
[12] "RADIATIONS.RADIATION.REGIMENINDICATION"
[13] "NUMBERPACKYEARSSMOKED"                 
[14] "YEAROFTOBACCOSMOKINGONSET"             
[15] "DISTANT.METASTASIS"                    
[16] "LYMPH.NODE.METASTASIS"                 
[17] "TUMOR.STAGECODE"                       
[18] "NEOPLASM.DISEASESTAGE"                 
[19] "BATCHNUMBER"                           

Input Data has 19 rows and 104 columns.

[1] "Batch" "19"   
[1] "Last Follow UP"
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
           1           21          485            3           NA           NA 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 
           1           27           NA            7           49          140 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
         293         1778         1636          412          922          763 
TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
        1357          336          223          109          125          179 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
         135          147         1536           21          329           92 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 
          14           33           19          196           36         2638 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
         585          269         1938          697         1313         1454 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
         658         1242          792          921          792          771 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
         403          329          232           29          364          240 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
          84         3759           NA         2948         2839           NA 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
        1864         1532         1516          799          612           NA 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
         232          213          217          115          353          414 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
        3950         1093         1142          744          418          114 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
         445           92         2428         2459         1556         1856 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 
        1669          471          178          160          208          977 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
        1257           NA          928         1059          387          445 
TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-HE-7128 TCGA-HE-7129 
         428         5558           NA          112           NA           NA 
TCGA-HE-7130 TCGA-J7-6720 
          NA           NA 
Variable 1:'AGE':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=86,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'NUMBERPACKYEARSSMOKED':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'DISTANT.METASTASIS':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'LYMPH.NODE.METASTASIS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'TUMOR.STAGECODE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NEOPLASM.DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'BATCH.NUMBER':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                         "GENDER"                     
[3] "KARNOFSKY.PERFORMANCE.SCORE" "DISTANT.METASTASIS"         
[5] "LYMPH.NODE.METASTASIS"       "TUMOR.STAGECODE"            
[7] "NEOPLASM.DISEASESTAGE"      
[1] "TUMOR.?STAGE" "6"           
[1] "stage2"
vv
 T1 T1A T1B  T2 T2A T2B  T3 T3A T3B  T4 
 10  34  14   9   3   1   6  18   8   1 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 104 columns, 1 survival variables, and 7 non-survival variables.
AGE, nv=39, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=4, binary=FALSE, numeric=TRUE
DISTANT.METASTASIS, nv=3, binary=FALSE, numeric=FALSE
LYMPH.NODE.METASTASIS, nv=4, binary=FALSE, numeric=FALSE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 16  4
  subtype2 31  3
  subtype3  8  1
  subtype4 15  4
  subtype5 13  2
subtype1 subtype2 subtype3 subtype4 subtype5 
      20       34        9       19       15 
subtype1 subtype2 subtype3 subtype4 subtype5 
       4        3        1        4        2 
$subtype1
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-AL-7173 TCGA-B1-7332 
        0.03         0.69         0.10        35.18        44.61         7.33 
TCGA-B9-4116 TCGA-BQ-5876 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5885 TCGA-BQ-5888 
        3.02        19.23        22.92        43.17        30.28        13.25 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-DW-5561 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-G7-6796 
        7.89         2.76        13.61        79.82        80.84        34.82 
TCGA-G7-7501 TCGA-GL-7966 
       14.63         3.68 

$subtype2
TCGA-A4-7288 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-AL-3467 TCGA-B3-4104 
       15.95         0.89         0.23         1.61        58.45         4.44 
TCGA-B3-8121 TCGA-B9-4114 TCGA-B9-4115 TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5883 
        4.83         0.69        10.82        86.73        63.72        40.83 
TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5889 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7049 
       26.04        26.04        10.82       123.58        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 
       61.28        50.37        49.84        26.27        11.28         7.63 
TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7839 TCGA-DW-7841 TCGA-DW-7842 
        7.13        11.61       129.86        13.74        14.63         3.02 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5903 TCGA-G7-6792 
       61.02        54.87         5.26        41.33 

$subtype3
TCGA-A4-7732 TCGA-AL-3472 TCGA-B3-3925 TCGA-B9-4113 TCGA-B9-4617 TCGA-DW-7837 
        0.03        30.31         3.58        50.50         1.08        37.55 
TCGA-DW-7840 TCGA-EV-5901 TCGA-G7-6795 
        3.75        15.48        30.51 

$subtype4
TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3473 TCGA-B1-5398 TCGA-B3-3926 TCGA-B9-4117 
        4.60         9.63        25.08        11.05         4.11         0.46 
TCGA-BQ-5877 TCGA-BQ-5882 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
        8.84        21.63        25.35         7.63         0.95        11.97 
TCGA-BQ-7056 TCGA-DW-7838 TCGA-EV-5902 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6797 
       20.12        24.46         5.85         6.84        11.05        12.72 
TCGA-G7-7502 
       14.07 

$subtype5
TCGA-AL-3468 TCGA-AL-3471 TCGA-B3-4103 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       53.79        13.55         5.88         0.62         6.44         1.18 
TCGA-BQ-5881 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7836 
       47.80        48.26        96.92         7.00         3.78        35.93 
TCGA-DZ-6133 TCGA-G7-6790 TCGA-GL-6846 
       51.16        32.12       182.73 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.03     0.23     0.03     0.46     0.62 
subtype1 subtype2 subtype3 subtype4 subtype5 
   80.84   129.86    50.50    25.35   182.73 
subtype1 subtype2 subtype3 subtype4 subtype5 
  14.120   20.995   15.480   11.050   32.120 
[1] "0.0 - 80.8 (14.1)"  "0.2 - 129.9 (21.0)" "0.0 - 50.5 (15.5)" 
[4] "0.5 - 25.4 (11.1)"  "0.6 - 182.7 (32.1)"
 [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype3"
 [7] "subtype2" "subtype2" "subtype2" "subtype4" "subtype4" "subtype2"
[13] "subtype5" "subtype5" "subtype3" "subtype4" "subtype1" "subtype4"
[19] "subtype1" "subtype3" "subtype4" "subtype5" "subtype2" "subtype2"
[25] "subtype3" "subtype2" "subtype2" "subtype1" "subtype4" "subtype3"
[31] "subtype5" "subtype5" "subtype5" "subtype2" "subtype1" "subtype4"
[37] "subtype2" "subtype1" "subtype1" "subtype5" "subtype4" "subtype2"
[43] "subtype2" "subtype1" "subtype2" "subtype4" "subtype1" "subtype2"
[49] "subtype4" "subtype4" "subtype4" "subtype1" "subtype1" "subtype2"
[55] "subtype5" "subtype5" "subtype2" "subtype2" "subtype2" "subtype2"
[61] "subtype2" "subtype2" "subtype4" "subtype2" "subtype2" "subtype5"
[67] "subtype2" "subtype5" "subtype2" "subtype1" "subtype2" "subtype5"
[73] "subtype3" "subtype4" "subtype2" "subtype3" "subtype2" "subtype2"
[79] "subtype1" "subtype1" "subtype5" "subtype2" "subtype2" "subtype3"
[85] "subtype4" "subtype2" "subtype4" "subtype5" "subtype2" "subtype4"
[91] "subtype3" "subtype1" "subtype4" "subtype1" "subtype4" "subtype5"
[97] "subtype1"
 [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype3"
 [7] "subtype2" "subtype2" "subtype2" "subtype4" "subtype4" "subtype2"
[13] "subtype5" "subtype5" "subtype3" "subtype4" "subtype1" "subtype4"
[19] "subtype1" "subtype3" "subtype4" "subtype5" "subtype2" "subtype2"
[25] "subtype3" "subtype2" "subtype2" "subtype1" "subtype4" "subtype3"
[31] "subtype5" "subtype5" "subtype5" "subtype2" "subtype1" "subtype4"
[37] "subtype2" "subtype1" "subtype1" "subtype5" "subtype4" "subtype2"
[43] "subtype2" "subtype1" "subtype2" "subtype4" "subtype1" "subtype2"
[49] "subtype4" "subtype4" "subtype4" "subtype1" "subtype1" "subtype2"
[55] "subtype5" "subtype5" "subtype2" "subtype2" "subtype2" "subtype2"
[61] "subtype2" "subtype2" "subtype4" "subtype2" "subtype2" "subtype5"
[67] "subtype2" "subtype5" "subtype2" "subtype1" "subtype2" "subtype5"
[73] "subtype3" "subtype4" "subtype2" "subtype3" "subtype2" "subtype2"
[79] "subtype1" "subtype1" "subtype5" "subtype2" "subtype2" "subtype3"
[85] "subtype4" "subtype2" "subtype4" "subtype5" "subtype2" "subtype4"
[91] "subtype3" "subtype1" "subtype4" "subtype1" "subtype4" "subtype5"
[97] "subtype1"
 [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype3"
 [7] "subtype2" "subtype2" "subtype2" "subtype4" "subtype4" "subtype2"
[13] "subtype5" "subtype5" "subtype3" "subtype4" "subtype1" "subtype4"
[19] "subtype1" "subtype3" "subtype4" "subtype5" "subtype2" "subtype2"
[25] "subtype3" "subtype2" "subtype2" "subtype1" "subtype4" "subtype3"
[31] "subtype5" "subtype5" "subtype5" "subtype2" "subtype1" "subtype4"
[37] "subtype2" "subtype1" "subtype1" "subtype5" "subtype4" "subtype2"
[43] "subtype2" "subtype1" "subtype2" "subtype4" "subtype1" "subtype2"
[49] "subtype4" "subtype4" "subtype4" "subtype1" "subtype1" "subtype2"
[55] "subtype5" "subtype5" "subtype2" "subtype2" "subtype2" "subtype2"
[61] "subtype2" "subtype2" "subtype4" "subtype2" "subtype2" "subtype5"
[67] "subtype2" "subtype5" "subtype2" "subtype1" "subtype2" "subtype5"
[73] "subtype3" "subtype4" "subtype2" "subtype3" "subtype2" "subtype2"
[79] "subtype1" "subtype1" "subtype5" "subtype2" "subtype2" "subtype3"
[85] "subtype4" "subtype2" "subtype4" "subtype5" "subtype2" "subtype4"
[91] "subtype3" "subtype1" "subtype4" "subtype1" "subtype4" "subtype5"
[97] "subtype1"
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype1  8 12
  subtype2 17 21
  subtype3  1  8
  subtype4  6 14
  subtype5  2 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   12
  subtype2   17   21
  subtype3    1    8
  subtype4    6   14
  subtype5    2   15
D1V4, continuous
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       4        7        3        6        2 
 [1] "subtype1" "subtype2" "subtype4" "subtype2" "subtype1" "subtype2"
 [7] "subtype3" "subtype4" "subtype2" "subtype3" "subtype2" "subtype2"
[13] "subtype3" "subtype4" "subtype2" "subtype4" "subtype1" "subtype4"
[19] "subtype1" "subtype4"
          vv
clus       M0 M1 MX
  subtype1  9  2  7
  subtype2 21  1 14
  subtype3  4  0  4
  subtype4 10  2  7
  subtype5 11  0  4
D1V5, multiclass
          vv
clus       N0 N1 N2 NX
  subtype1  5  6  1  8
  subtype2  5  2  1 30
  subtype3  1  0  0  8
  subtype4  7  3  2  8
  subtype5  2  1  0 14
D1V6, multiclass
D1V7, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       7        1         7        3
  subtype2      23        4         7        1
  subtype3       5        0         1        0
  subtype4       7        1         7        4
  subtype5      11        1         2        1
D1V8, multiclass

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 15  4
  subtype2 34  2
  subtype3 20  6
subtype1 subtype2 subtype3 
      19       36       26 
subtype1 subtype2 subtype3 
       4        2        6 
$subtype1
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7585 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-8121 
        0.03         0.69        35.18        44.61        11.05         4.83 
TCGA-BQ-5880 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-7049 
       43.17        40.83        26.04        13.25        10.82        44.84 
TCGA-BQ-7055 TCGA-BQ-7059 TCGA-DW-7838 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5903 
       26.27         7.63        24.46        80.84        61.02         5.26 
TCGA-G7-6796 
       34.82 

$subtype2
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-B1-7332 
       15.95         0.10         0.03         0.89         1.61         7.33 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5881 TCGA-BQ-5885 TCGA-BQ-7045 
        0.62         6.44         1.18        47.80        30.28        48.26 
TCGA-BQ-7046 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7060 TCGA-BQ-7062 
       96.92        61.28        50.37        49.84         7.00         3.78 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7839 
       11.61        13.61       129.86        35.93        37.55        13.74 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
        3.75        14.63         3.02        51.16        54.87        15.48 
TCGA-EV-5902 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7502 
        5.85        32.12        41.33        30.51        12.72        14.07 

$subtype3
TCGA-A4-7915 TCGA-A4-8098 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        0.23         4.60        86.73        19.23         8.84        63.72 
TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 
       22.92        21.63        26.04        25.35         7.63         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7056 
       11.97         7.89         2.76       123.58        93.34        20.12 
TCGA-BQ-7058 TCGA-BQ-7061 TCGA-DZ-6131 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7501 
       11.28         7.13        79.82         6.84        11.05        14.63 
TCGA-GL-6846 TCGA-GL-7966 
      182.73         3.68 

subtype1 subtype2 subtype3 
    0.03     0.03     0.23 
subtype1 subtype2 subtype3 
   80.84   129.86   182.73 
subtype1 subtype2 subtype3 
   26.04    14.35    13.30 
[1] "0.0 - 80.8 (26.0)"  "0.0 - 129.9 (14.4)" "0.2 - 182.7 (13.3)"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [7] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
[13] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
[19] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
[25] "subtype3" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
[31] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[37] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
[43] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype3"
[49] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[55] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[61] "subtype2" "subtype2" "subtype3" "subtype1" "subtype2" "subtype1"
[67] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype2"
[73] "subtype2" "subtype3" "subtype2" "subtype1" "subtype2" "subtype3"
[79] "subtype2" "subtype3" "subtype3"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [7] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
[13] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
[19] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
[25] "subtype3" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
[31] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[37] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
[43] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype3"
[49] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[55] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[61] "subtype2" "subtype2" "subtype3" "subtype1" "subtype2" "subtype1"
[67] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype2"
[73] "subtype2" "subtype3" "subtype2" "subtype1" "subtype2" "subtype3"
[79] "subtype2" "subtype3" "subtype3"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [7] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
[13] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
[19] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
[25] "subtype3" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
[31] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[37] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
[43] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype3"
[49] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[55] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[61] "subtype2" "subtype2" "subtype3" "subtype1" "subtype2" "subtype1"
[67] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype2"
[73] "subtype2" "subtype3" "subtype2" "subtype1" "subtype2" "subtype3"
[79] "subtype2" "subtype3" "subtype3"
D2V2, continuous
D2V3, binary
          cls
clus        0  1
  subtype1  8 13
  subtype2 10 30
  subtype3 12 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   13
  subtype2   10   30
  subtype3   12   15
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        8       10       12
  MALE         13       30       15
D2V4, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 
       5       14        2 
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[19] "subtype2"
          vv
clus       M0 M1 MX
  subtype1 12  1  7
  subtype2 17  0 21
  subtype3 16  3  8
D2V5, multiclass
          vv
clus       N0 N1 N2 NX
  subtype1  3  2  1 15
  subtype2  8  0  0 32
  subtype3  9  8  3  7
D2V6, multiclass
D2V7, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      14        1         3        2
  subtype2      30        3         4        0
  subtype3       4        1        16        6
D2V8, multiclass

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 21  3
  subtype2 15  8
  subtype3 23  2
subtype1 subtype2 subtype3 
      24       23       25 
subtype1 subtype2 subtype3 
       3        8        2 
$subtype1
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       53.79        13.55        30.31         3.58         4.11         5.88 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-BQ-7045 
       50.50         0.69        10.82         0.46         1.08        48.26 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
        3.78        11.61        13.61        51.16        54.87        15.48 
TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7502 
        5.85         5.26        41.33        30.51        12.72        14.07 

$subtype2
TCGA-AL-3466 TCGA-AL-3467 TCGA-B3-4104 TCGA-B9-4116 TCGA-BQ-5877 TCGA-BQ-5879 
        9.63        58.45         4.44         3.02         8.84        22.92 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5891 
       21.63        40.83        25.35        13.25        10.82         0.95 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7053 TCGA-DZ-6131 
        7.89         2.76        93.34        44.84        49.84        79.82 
TCGA-DZ-6132 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7501 TCGA-GL-7966 
       80.84         6.84        11.05        14.63         3.68 

$subtype3
TCGA-AL-3473 TCGA-B1-5398 TCGA-B9-5156 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5880 
       25.08        11.05         6.44        19.23        63.72        43.17 
TCGA-BQ-5881 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-5892 
       47.80        26.04        30.28        26.04         7.63        11.97 
TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7056 TCGA-BQ-7058 
      123.58        96.92        61.28        50.37        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-DZ-6134 TCGA-G7-6790 TCGA-G7-6796 
        7.63         7.00         7.13        61.02        32.12        34.82 
TCGA-GL-6846 
      182.73 

subtype1 subtype2 subtype3 
    0.46     0.95     6.44 
subtype1 subtype2 subtype3 
   54.87    93.34   182.73 
subtype1 subtype2 subtype3 
  13.135   13.250   26.040 
[1] "0.5 - 54.9 (13.1)"  "0.9 - 93.3 (13.2)"  "6.4 - 182.7 (26.0)"
 [1] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
 [7] "subtype3" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[13] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype3"
[19] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[25] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
[31] "subtype2" "subtype2" "subtype3" "subtype2" "subtype3" "subtype2"
[37] "subtype2" "subtype3" "subtype1" "subtype3" "subtype2" "subtype2"
[43] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[49] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype2"
[55] "subtype2" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[61] "subtype1" "subtype2" "subtype3" "subtype1" "subtype2" "subtype1"
[67] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
 [1] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
 [7] "subtype3" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[13] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype3"
[19] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[25] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
[31] "subtype2" "subtype2" "subtype3" "subtype2" "subtype3" "subtype2"
[37] "subtype2" "subtype3" "subtype1" "subtype3" "subtype2" "subtype2"
[43] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[49] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype2"
[55] "subtype2" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[61] "subtype1" "subtype2" "subtype3" "subtype1" "subtype2" "subtype1"
[67] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
 [1] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
 [7] "subtype3" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[13] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype3"
[19] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[25] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
[31] "subtype2" "subtype2" "subtype3" "subtype2" "subtype3" "subtype2"
[37] "subtype2" "subtype3" "subtype1" "subtype3" "subtype2" "subtype2"
[43] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[49] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype2"
[55] "subtype2" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[61] "subtype1" "subtype2" "subtype3" "subtype1" "subtype2" "subtype1"
[67] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
D3V2, continuous
D3V3, binary
          cls
clus        0  1
  subtype1  5 21
  subtype2 13 11
  subtype3  5 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   21
  subtype2   13   11
  subtype3    5   20
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        5       13        5
  MALE         21       11       20
D3V4, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 
       7        3        2 
 [1] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [7] "subtype2" "subtype1" "subtype2" "subtype1"
          vv
clus       M0 M1 MX
  subtype1 15  0  7
  subtype2 12  5  6
  subtype3 20  0  4
D3V5, multiclass
          vv
clus       N0 N1 N2 NX
  subtype1  2  0  0 24
  subtype2  6  8  2  8
  subtype3  7  4  1 13
D3V6, multiclass
D3V7, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      19        0         2        0
  subtype2       4        1        10        7
  subtype3      12        2         9        1
D3V8, multiclass

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 11  6
  subtype2 31  3
  subtype3 17  4
subtype1 subtype2 subtype3 
      17       34       21 
subtype1 subtype2 subtype3 
       6        3        4 
$subtype1
TCGA-AL-3467 TCGA-B3-4104 TCGA-B9-4116 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5883 
       58.45         4.44         3.02         8.84        22.92        40.83 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7049 TCGA-DZ-6132 
       13.25        10.82         7.89         2.76        44.84        80.84 
TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6793 TCGA-GL-7966 
       15.48         5.26         6.84        11.05         3.68 

$subtype2
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-3926 
       53.79        13.55        30.31        11.05         3.58         4.11 
TCGA-B3-4103 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 
        5.88        50.50         0.69        10.82         0.46         1.08 
TCGA-B9-5156 TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 
        6.44        47.80        26.04        48.26        96.92        50.37 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DZ-6133 
        7.63         7.00         3.78        11.61        13.61        51.16 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5902 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
       61.02        54.87         5.85        32.12        41.33        30.51 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 TCGA-GL-6846 
       34.82        12.72        14.07       182.73 

$subtype3
TCGA-AL-3466 TCGA-AL-3473 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5882 
        9.63        25.08        19.23        63.72        43.17        21.63 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       26.04        30.28        25.35         7.63         0.95        11.97 
TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7058 
      123.58        93.34        61.28        49.84        20.12        11.28 
TCGA-BQ-7061 TCGA-DZ-6131 TCGA-G7-7501 
        7.13        79.82        14.63 

subtype1 subtype2 subtype3 
    2.76     0.46     0.95 
subtype1 subtype2 subtype3 
   80.84   182.73   123.58 
subtype1 subtype2 subtype3 
   10.82    13.84    25.08 
[1] "2.8 - 80.8 (10.8)"  "0.5 - 182.7 (13.8)" "0.9 - 123.6 (25.1)"
 [1] "subtype3" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[13] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[19] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype2"
[25] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
[31] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1"
[37] "subtype1" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
[43] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
[49] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[55] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[61] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[67] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
 [1] "subtype3" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[13] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[19] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype2"
[25] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
[31] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1"
[37] "subtype1" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
[43] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
[49] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[55] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[61] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[67] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
 [1] "subtype3" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[13] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[19] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype2"
[25] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
[31] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1"
[37] "subtype1" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
[43] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
[49] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[55] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[61] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[67] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
D4V2, continuous
D4V3, binary
          cls
clus        0  1
  subtype1 11  7
  subtype2  4 32
  subtype3  8 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11    7
  subtype2    4   32
  subtype3    8   13
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       11        4        8
  MALE          7       32       13
D4V4, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 
       3        7        2 
 [1] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
 [7] "subtype1" "subtype2" "subtype2" "subtype2"
          vv
clus       M0 M1 MX
  subtype1  9  4  4
  subtype2 20  0 11
  subtype3 18  1  2
D4V5, multiclass
          vv
clus       N0 N1 N2 NX
  subtype1  1  6  2  9
  subtype2  4  1  0 31
  subtype3 10  5  1  5
D4V6, multiclass
D4V7, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       6        1         3        6
  subtype2      24        1         4        1
  subtype3       5        1        14        1
D4V8, multiclass

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 21  2
  subtype2 29  6
  subtype3 20  2
  subtype4 13  4
subtype1 subtype2 subtype3 subtype4 
      23       35       22       17 
subtype1 subtype2 subtype3 subtype4 
       2        6        2        4 
$subtype1
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7996 TCGA-AL-3468 
        0.03        15.95         0.10         0.03         1.61        53.79 
TCGA-AL-3471 TCGA-B3-3926 TCGA-B3-4103 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       13.55         4.11         5.88        50.50         0.69        10.82 
TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-7268 TCGA-BQ-5888 TCGA-BQ-7046 
        3.02         1.08         0.62         1.18        13.25        96.92 
TCGA-BQ-7055 TCGA-DW-7842 TCGA-DZ-6133 TCGA-EV-5902 TCGA-G7-6797 
       26.27         3.02        51.16         5.85        12.72 

$subtype2
TCGA-A4-7287 TCGA-A4-7734 TCGA-A4-7915 TCGA-AL-3466 TCGA-AL-3472 TCGA-AL-7173 
        0.69         0.89         0.23         9.63        30.31        44.61 
TCGA-B3-4104 TCGA-B3-8121 TCGA-BQ-5876 TCGA-BQ-5879 TCGA-BQ-5883 TCGA-BQ-5887 
        4.44         4.83        19.23        22.92        40.83        25.35 
TCGA-BQ-5889 TCGA-BQ-5894 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7053 
       10.82         2.76        48.26        93.34        44.84        49.84 
TCGA-BQ-7056 TCGA-BQ-7060 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12         7.00        11.61        13.61       129.86        35.93 
TCGA-DW-7838 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6789 
       24.46        80.84        61.02        15.48         5.26         6.84 
TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 
       11.05        34.82        14.07       182.73         3.68 

$subtype3
TCGA-A4-7585 TCGA-A4-8098 TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3925 
       35.18         4.60        25.08        11.05         7.33         3.58 
TCGA-B9-5156 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5890 
        6.44        63.72        43.17        47.80        26.04         7.63 
TCGA-BQ-5892 TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7062 TCGA-DW-7837 TCGA-DW-7840 
       11.97        50.37         7.63         3.78        37.55         3.75 
TCGA-DW-7841 TCGA-DZ-6135 TCGA-G7-6790 TCGA-G7-6792 
       14.63        54.87        32.12        41.33 

$subtype4
TCGA-AL-3467 TCGA-B9-4117 TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5882 TCGA-BQ-5884 
       58.45         0.46        86.73         8.84        21.63        26.04 
TCGA-BQ-5885 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7050 TCGA-BQ-7058 
       30.28         0.95         7.89       123.58        61.28        11.28 
TCGA-BQ-7061 TCGA-DW-7839 TCGA-DZ-6131 TCGA-G7-6795 TCGA-G7-7501 
        7.13        13.74        79.82        30.51        14.63 

subtype1 subtype2 subtype3 subtype4 
    0.03     0.23     3.58     0.46 
subtype1 subtype2 subtype3 subtype4 
   96.92   182.73    63.72   123.58 
subtype1 subtype2 subtype3 subtype4 
   5.850   19.230   19.855   21.630 
[1] "0.0 - 96.9 (5.8)"   "0.2 - 182.7 (19.2)" "3.6 - 63.7 (19.9)" 
[4] "0.5 - 123.6 (21.6)"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
 [7] "subtype2" "subtype2" "subtype1" "subtype3" "subtype2" "subtype4"
[13] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype3"
[19] "subtype3" "subtype3" "subtype1" "subtype1" "subtype2" "subtype2"
[25] "subtype1" "subtype1" "subtype1" "subtype1" "subtype4" "subtype1"
[31] "subtype1" "subtype3" "subtype1" "subtype4" "subtype2" "subtype4"
[37] "subtype3" "subtype2" "subtype3" "subtype3" "subtype4" "subtype2"
[43] "subtype4" "subtype4" "subtype3" "subtype2" "subtype1" "subtype2"
[49] "subtype3" "subtype4" "subtype3" "subtype4" "subtype2" "subtype4"
[55] "subtype2" "subtype1" "subtype2" "subtype2" "subtype4" "subtype3"
[61] "subtype2" "subtype1" "subtype2" "subtype4" "subtype3" "subtype2"
[67] "subtype4" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[73] "subtype3" "subtype2" "subtype4" "subtype3" "subtype3" "subtype1"
[79] "subtype4" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
[85] "subtype1" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
[91] "subtype4" "subtype2" "subtype1" "subtype4" "subtype2" "subtype2"
[97] "subtype2"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
 [7] "subtype2" "subtype2" "subtype1" "subtype3" "subtype2" "subtype4"
[13] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype3"
[19] "subtype3" "subtype3" "subtype1" "subtype1" "subtype2" "subtype2"
[25] "subtype1" "subtype1" "subtype1" "subtype1" "subtype4" "subtype1"
[31] "subtype1" "subtype3" "subtype1" "subtype4" "subtype2" "subtype4"
[37] "subtype3" "subtype2" "subtype3" "subtype3" "subtype4" "subtype2"
[43] "subtype4" "subtype4" "subtype3" "subtype2" "subtype1" "subtype2"
[49] "subtype3" "subtype4" "subtype3" "subtype4" "subtype2" "subtype4"
[55] "subtype2" "subtype1" "subtype2" "subtype2" "subtype4" "subtype3"
[61] "subtype2" "subtype1" "subtype2" "subtype4" "subtype3" "subtype2"
[67] "subtype4" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[73] "subtype3" "subtype2" "subtype4" "subtype3" "subtype3" "subtype1"
[79] "subtype4" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
[85] "subtype1" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
[91] "subtype4" "subtype2" "subtype1" "subtype4" "subtype2" "subtype2"
[97] "subtype2"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
 [7] "subtype2" "subtype2" "subtype1" "subtype3" "subtype2" "subtype4"
[13] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype3"
[19] "subtype3" "subtype3" "subtype1" "subtype1" "subtype2" "subtype2"
[25] "subtype1" "subtype1" "subtype1" "subtype1" "subtype4" "subtype1"
[31] "subtype1" "subtype3" "subtype1" "subtype4" "subtype2" "subtype4"
[37] "subtype3" "subtype2" "subtype3" "subtype3" "subtype4" "subtype2"
[43] "subtype4" "subtype4" "subtype3" "subtype2" "subtype1" "subtype2"
[49] "subtype3" "subtype4" "subtype3" "subtype4" "subtype2" "subtype4"
[55] "subtype2" "subtype1" "subtype2" "subtype2" "subtype4" "subtype3"
[61] "subtype2" "subtype1" "subtype2" "subtype4" "subtype3" "subtype2"
[67] "subtype4" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[73] "subtype3" "subtype2" "subtype4" "subtype3" "subtype3" "subtype1"
[79] "subtype4" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
[85] "subtype1" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
[91] "subtype4" "subtype2" "subtype1" "subtype4" "subtype2" "subtype2"
[97] "subtype2"
D5V2, continuous
D5V3, binary
          cls
clus        0  1
  subtype1  7 21
  subtype2 16 21
  subtype3  2 20
  subtype4  9  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   21
  subtype2   16   21
  subtype3    2   20
  subtype4    9    8
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        7       16        2        9
  MALE         21       21       20        8
D5V4, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       4       12        4        2 
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
[13] "subtype2" "subtype1" "subtype2" "subtype3" "subtype2" "subtype2"
[19] "subtype1" "subtype2"
          vv
clus       M0 M1 MX
  subtype1 13  0  9
  subtype2 19  3 15
  subtype3 13  0  8
  subtype4 10  2  4
D5V5, multiclass
          vv
clus       N0 N1 N2 NX
  subtype1  3  0  0 25
  subtype2  6  6  3 22
  subtype3  5  3  0 14
  subtype4  6  3  1  7
D5V6, multiclass
D5V7, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      17        1         3        0
  subtype2      20        3         6        7
  subtype3      11        3         7        0
  subtype4       5        0         8        2
D5V8, multiclass

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 28  5
  subtype2 23  6
  subtype3  8  1
  subtype4 24  2
subtype1 subtype2 subtype3 subtype4 
      33       29        9       26 
subtype1 subtype2 subtype3 subtype4 
       5        6        1        2 
$subtype1
TCGA-A4-7287 TCGA-A4-7734 TCGA-A4-7915 TCGA-AL-3472 TCGA-AL-7173 TCGA-B3-4104 
        0.69         0.89         0.23        30.31        44.61         4.44 
TCGA-B3-8121 TCGA-BQ-5879 TCGA-BQ-5883 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
        4.83        22.92        40.83        25.35        13.25        10.82 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7053 TCGA-BQ-7055 
        7.89         2.76        93.34        44.84        49.84        26.27 
TCGA-BQ-7056 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 TCGA-DW-7842 
       20.12        11.61       129.86        35.93        24.46         3.02 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6793 
       80.84        61.02        15.48         5.26         6.84        11.05 
TCGA-G7-6796 TCGA-G7-7502 TCGA-GL-7966 
       34.82        14.07         3.68 

$subtype2
TCGA-A4-7585 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3473 TCGA-B1-5398 TCGA-B3-3925 
       35.18         4.60         9.63        25.08        11.05         3.58 
TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5884 
       86.73         8.84        63.72        43.17        21.63        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7051 
       30.28        26.04         7.63         0.95        11.97        50.37 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7840 
       11.28         7.63         7.13        13.61        37.55         3.75 
TCGA-DW-7841 TCGA-DZ-6131 TCGA-DZ-6135 TCGA-G7-6792 TCGA-G7-7501 
       14.63        79.82        54.87        41.33        14.63 

$subtype3
TCGA-B9-5156 TCGA-BQ-5876 TCGA-BQ-5881 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7060 
        6.44        19.23        47.80        48.26        96.92         7.00 
TCGA-BQ-7062 TCGA-G7-6790 TCGA-GL-6846 
        3.78        32.12       182.73 

$subtype4
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7996 TCGA-AL-3467 
        0.03        15.95         0.10         0.03         1.61        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-B1-7332 TCGA-B3-3926 TCGA-B3-4103 TCGA-B9-4113 
       53.79        13.55         7.33         4.11         5.88        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
        0.69        10.82         3.02         0.46         1.08         0.62 
TCGA-B9-7268 TCGA-BQ-7044 TCGA-BQ-7050 TCGA-DW-7839 TCGA-DZ-6133 TCGA-EV-5902 
        1.18       123.58        61.28        13.74        51.16         5.85 
TCGA-G7-6795 TCGA-G7-6797 
       30.51        12.72 

subtype1 subtype2 subtype3 subtype4 
    0.23     0.95     3.78     0.03 
subtype1 subtype2 subtype3 subtype4 
  129.86    86.73   182.73   123.58 
subtype1 subtype2 subtype3 subtype4 
  15.480   14.630   32.120    6.605 
[1] "0.2 - 129.9 (15.5)" "0.9 - 86.7 (14.6)"  "3.8 - 182.7 (32.1)"
[4] "0.0 - 123.6 (6.6)" 
 [1] "subtype4" "subtype1" "subtype4" "subtype4" "subtype2" "subtype4"
 [7] "subtype1" "subtype1" "subtype4" "subtype2" "subtype2" "subtype4"
[13] "subtype4" "subtype4" "subtype1" "subtype2" "subtype1" "subtype2"
[19] "subtype4" "subtype2" "subtype4" "subtype4" "subtype1" "subtype1"
[25] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[31] "subtype4" "subtype3" "subtype4" "subtype2" "subtype3" "subtype2"
[37] "subtype2" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
[43] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[49] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype4"
[55] "subtype3" "subtype3" "subtype1" "subtype1" "subtype4" "subtype2"
[61] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
[67] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
[73] "subtype2" "subtype1" "subtype4" "subtype2" "subtype2" "subtype1"
[79] "subtype2" "subtype1" "subtype4" "subtype1" "subtype2" "subtype1"
[85] "subtype4" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
[91] "subtype4" "subtype1" "subtype4" "subtype2" "subtype1" "subtype3"
[97] "subtype1"
 [1] "subtype4" "subtype1" "subtype4" "subtype4" "subtype2" "subtype4"
 [7] "subtype1" "subtype1" "subtype4" "subtype2" "subtype2" "subtype4"
[13] "subtype4" "subtype4" "subtype1" "subtype2" "subtype1" "subtype2"
[19] "subtype4" "subtype2" "subtype4" "subtype4" "subtype1" "subtype1"
[25] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[31] "subtype4" "subtype3" "subtype4" "subtype2" "subtype3" "subtype2"
[37] "subtype2" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
[43] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[49] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype4"
[55] "subtype3" "subtype3" "subtype1" "subtype1" "subtype4" "subtype2"
[61] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
[67] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
[73] "subtype2" "subtype1" "subtype4" "subtype2" "subtype2" "subtype1"
[79] "subtype2" "subtype1" "subtype4" "subtype1" "subtype2" "subtype1"
[85] "subtype4" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
[91] "subtype4" "subtype1" "subtype4" "subtype2" "subtype1" "subtype3"
[97] "subtype1"
 [1] "subtype4" "subtype1" "subtype4" "subtype4" "subtype2" "subtype4"
 [7] "subtype1" "subtype1" "subtype4" "subtype2" "subtype2" "subtype4"
[13] "subtype4" "subtype4" "subtype1" "subtype2" "subtype1" "subtype2"
[19] "subtype4" "subtype2" "subtype4" "subtype4" "subtype1" "subtype1"
[25] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[31] "subtype4" "subtype3" "subtype4" "subtype2" "subtype3" "subtype2"
[37] "subtype2" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
[43] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[49] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype4"
[55] "subtype3" "subtype3" "subtype1" "subtype1" "subtype4" "subtype2"
[61] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
[67] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
[73] "subtype2" "subtype1" "subtype4" "subtype2" "subtype2" "subtype1"
[79] "subtype2" "subtype1" "subtype4" "subtype1" "subtype2" "subtype1"
[85] "subtype4" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
[91] "subtype4" "subtype1" "subtype4" "subtype2" "subtype1" "subtype3"
[97] "subtype1"
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype1 18 19
  subtype2  6 23
  subtype3  0 10
  subtype4 10 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   19
  subtype2    6   23
  subtype3    0   10
  subtype4   10   18
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       18        6        0       10
  MALE         19       23       10       18
D6V4, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 
      11        6        1        4 
 [1] "subtype4" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
 [7] "subtype1" "subtype2" "subtype1" "subtype4" "subtype2" "subtype2"
[13] "subtype1" "subtype1" "subtype4" "subtype1" "subtype1" "subtype1"
[19] "subtype4" "subtype2" "subtype1"
          vv
clus       M0 M1 MX
  subtype1 18  3 16
  subtype2 19  2  8
  subtype3  6  0  3
  subtype4 12  0  9
D6V5, multiclass
          vv
clus       N0 N1 N2 NX
  subtype1  6  5  3 23
  subtype2  9  6  1 13
  subtype3  1  1  0  8
  subtype4  4  0  0 24
D6V6, multiclass
D6V7, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      20        3         7        6
  subtype2      11        2        14        2
  subtype3       8        0         0        1
  subtype4      14        2         3        0
D6V8, multiclass

Clustering(7) Variable = MIRSEQ_MATURE_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 25  4
  subtype2 27  6
  subtype3 17  2
subtype1 subtype2 subtype3 
      29       33       19 
subtype1 subtype2 subtype3 
       4        6        2 
$subtype1
TCGA-A4-7286 TCGA-A4-7585 TCGA-A4-8098 TCGA-B1-5398 TCGA-B1-7332 TCGA-B9-5156 
        0.03        35.18         4.60        11.05         7.33         6.44 
TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5884 
       86.73        63.72        43.17        47.80        21.63        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7044 
       30.28        26.04         7.63         0.95        11.97       123.58 
TCGA-BQ-7046 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7062 
       96.92        61.28        50.37        11.28         7.63         3.78 
TCGA-DW-7840 TCGA-DZ-6131 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-7501 
        3.75        79.82        32.12        41.33        14.63 

$subtype2
TCGA-A4-7287 TCGA-A4-7734 TCGA-A4-7915 TCGA-AL-7173 TCGA-B3-8121 TCGA-BQ-5876 
        0.69         0.89         0.23        44.61         4.83        19.23 
TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5883 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5894 
        8.84        22.92        40.83        25.35        10.82         2.76 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7060 
       48.26        93.34        44.84        49.84        20.12         7.00 
TCGA-BQ-7061 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 TCGA-DZ-6132 TCGA-DZ-6134 
        7.13       129.86        35.93        24.46        80.84        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6796 
       54.87        15.48         5.26         6.84        11.05        34.82 
TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 
       14.07       182.73         3.68 

$subtype3
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7996 TCGA-B9-5155 TCGA-B9-7268 
       15.95         0.10         0.03         1.61         0.62         1.18 
TCGA-BQ-5888 TCGA-BQ-5893 TCGA-BQ-7055 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7837 
       13.25         7.89        26.27        11.61        13.61        37.55 
TCGA-DW-7839 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6133 TCGA-EV-5902 TCGA-G7-6795 
       13.74        14.63         3.02        51.16         5.85        30.51 
TCGA-G7-6797 
       12.72 

subtype1 subtype2 subtype3 
    0.03     0.23     0.03 
subtype1 subtype2 subtype3 
  123.58   182.73    51.16 
subtype1 subtype2 subtype3 
   26.04    20.12    12.72 
[1] "0.0 - 123.6 (26.0)" "0.2 - 182.7 (20.1)" "0.0 - 51.2 (12.7)" 
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
 [7] "subtype2" "subtype2" "subtype3" "subtype1" "subtype2" "subtype1"
[13] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype1"
[19] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[25] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
[31] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
[37] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
[43] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
[49] "subtype1" "subtype2" "subtype2" "subtype1" "subtype3" "subtype3"
[55] "subtype2" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
[61] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
[67] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
[73] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
[79] "subtype2" "subtype2" "subtype2"
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
 [7] "subtype2" "subtype2" "subtype3" "subtype1" "subtype2" "subtype1"
[13] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype1"
[19] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[25] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
[31] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
[37] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
[43] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
[49] "subtype1" "subtype2" "subtype2" "subtype1" "subtype3" "subtype3"
[55] "subtype2" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
[61] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
[67] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
[73] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
[79] "subtype2" "subtype2" "subtype2"
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
 [7] "subtype2" "subtype2" "subtype3" "subtype1" "subtype2" "subtype1"
[13] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype1"
[19] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[25] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
[31] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
[37] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
[43] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
[49] "subtype1" "subtype2" "subtype2" "subtype1" "subtype3" "subtype3"
[55] "subtype2" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
[61] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
[67] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
[73] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
[79] "subtype2" "subtype2" "subtype2"
D7V2, continuous
D7V3, binary
          cls
clus        0  1
  subtype1  7 23
  subtype2 16 19
  subtype3  7 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   23
  subtype2   16   19
  subtype3    7   16
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        7       16        7
  MALE         23       19       16
D7V4, continuous
          vv
clus       M0 M1 MX
  subtype1 20  0  8
  subtype2 16  3 16
  subtype3  9  1 12
D7V5, multiclass
          vv
clus       N0 N1 N2 NX
  subtype1 10  3  1 16
  subtype2  6  6  3 20
  subtype3  4  1  0 18
D7V6, multiclass
D7V7, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      12        2        14        0
  subtype2      20        2         6        7
  subtype3      16        1         3        1
D7V8, multiclass

Clustering(8) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 32  1
  subtype2 10  5
  subtype3 27  6
subtype1 subtype2 subtype3 
      33       15       33 
subtype1 subtype2 subtype3 
       1        5        6 
$subtype1
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7996 TCGA-B1-5398 
        0.03        15.95         0.10         0.03         1.61        11.05 
TCGA-B1-7332 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5876 TCGA-BQ-5881 
        7.33         0.62         6.44         1.18        19.23        47.80 
TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7050 
       26.04        26.04         7.63       123.58        96.92        61.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7839 
        7.63         7.00         3.78        13.61        37.55        13.74 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5902 TCGA-G7-6790 
        3.75        14.63        51.16        54.87         5.85        32.12 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 
       41.33        30.51        12.72 

$subtype2
TCGA-A4-7585 TCGA-A4-8098 TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 
       35.18         4.60        86.73         8.84        63.72        43.17 
TCGA-BQ-5882 TCGA-BQ-5885 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7051 TCGA-BQ-7058 
       21.63        30.28         0.95        11.97        50.37        11.28 
TCGA-BQ-7061 TCGA-DZ-6131 TCGA-G7-7501 
        7.13        79.82        14.63 

$subtype3
TCGA-A4-7287 TCGA-A4-7734 TCGA-A4-7915 TCGA-AL-7173 TCGA-B3-8121 TCGA-BQ-5879 
        0.69         0.89         0.23        44.61         4.83        22.92 
TCGA-BQ-5883 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5893 TCGA-BQ-5894 
       40.83        25.35        13.25        10.82         7.89         2.76 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       48.26        93.34        44.84        49.84        26.27        20.12 
TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 TCGA-DW-7842 TCGA-DZ-6132 
       11.61       129.86        35.93        24.46         3.02        80.84 
TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6796 
       61.02        15.48         5.26         6.84        11.05        34.82 
TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 
       14.07       182.73         3.68 

subtype1 subtype2 subtype3 
    0.03     0.95     0.23 
subtype1 subtype2 subtype3 
  123.58    86.73   182.73 
subtype1 subtype2 subtype3 
   13.61    21.63    20.12 
[1] "0.0 - 123.6 (13.6)" "0.9 - 86.7 (21.6)"  "0.2 - 182.7 (20.1)"
 [1] "subtype1" "subtype3" "subtype1" "subtype1" "subtype2" "subtype1"
 [7] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype1"
[13] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype2"
[19] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
[25] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
[31] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype3"
[37] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
[43] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
[49] "subtype1" "subtype1" "subtype2" "subtype1" "subtype3" "subtype1"
[55] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[61] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
[67] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
[73] "subtype1" "subtype3" "subtype1" "subtype3" "subtype1" "subtype2"
[79] "subtype3" "subtype3" "subtype3"
 [1] "subtype1" "subtype3" "subtype1" "subtype1" "subtype2" "subtype1"
 [7] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype1"
[13] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype2"
[19] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
[25] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
[31] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype3"
[37] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
[43] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
[49] "subtype1" "subtype1" "subtype2" "subtype1" "subtype3" "subtype1"
[55] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[61] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
[67] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
[73] "subtype1" "subtype3" "subtype1" "subtype3" "subtype1" "subtype2"
[79] "subtype3" "subtype3" "subtype3"
 [1] "subtype1" "subtype3" "subtype1" "subtype1" "subtype2" "subtype1"
 [7] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype1"
[13] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype2"
[19] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
[25] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
[31] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype3"
[37] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
[43] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
[49] "subtype1" "subtype1" "subtype2" "subtype1" "subtype3" "subtype1"
[55] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[61] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
[67] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
[73] "subtype1" "subtype3" "subtype1" "subtype3" "subtype1" "subtype2"
[79] "subtype3" "subtype3" "subtype3"
D8V2, continuous
D8V3, binary
          cls
clus        0  1
  subtype1  7 30
  subtype2  5 10
  subtype3 18 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   30
  subtype2    5   10
  subtype3   18   18
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        7        5       18
  MALE         30       10       18
D8V4, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 subtype3 
       9        1       11 
 [1] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [7] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
[13] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
[19] "subtype1" "subtype3"
          vv
clus       M0 M1 MX
  subtype1 17  0 17
  subtype2 11  1  3
  subtype3 17  3 16
D8V5, multiclass
          vv
clus       N0 N1 N2 NX
  subtype1  6  0  0 31
  subtype2  7  4  1  3
  subtype3  7  6  3 20
D8V6, multiclass
D8V7, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      25        2         6        0
  subtype2       3        1        10        1
  subtype3      20        2         7        7
D8V8, multiclass
                         V1.D                            V2 
              "Time to Death"                         "AGE" 
                           V3                            V4 
                     "GENDER" "KARNOFSKY.PERFORMANCE.SCORE" 
                           V5                            V6 
         "DISTANT.METASTASIS"       "LYMPH.NODE.METASTASIS" 
                           V7                            V8 
            "TUMOR.STAGECODE"       "NEOPLASM.DISEASESTAGE" 
> q(save="no")
