[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTPCPG-TP"
[1] "opt"                    "-OPAGGREGRATED_CLUSTER"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/PCPG-TP/10006138/PCPG-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PCPG-TP/10667976/PCPG-TP.mergedcluster.txt"

nPatients in clinical file=61, in cluster file=179, common to both=61
[1]  8 61
[1] "CN_CNMF"
[1] 3
 1  2  3  4  5 
 4  7 21 18  7 
 1  2  3  4  5 
 4  7 21 18  7 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
14 28 19 
 1  2  3 
14 28 19 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4 
13 21 18  9 
 1  2  3  4 
13 21 18  9 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
14 25 13  9 
 1  2  3  4 
14 25 13  9 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
25 20 16 
 1  2  3 
25 20 16 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
23 22  6 10 
 1  2  3  4 
23 22  6 10 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
14 24 23 
 1  2  3 
14 24 23 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3 
24 21 16 
 1  2  3 
24 21 16 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "DCCUPLOADDATE"                         
 [6] "GENDER"                                
 [7] "RADIATIONTHERAPY"                      
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "RACE"                                  
[10] "ETHNICITY"                             
[11] "BATCHNUMBER"                           

Input Data has 11 rows and 61 columns.

[1] "Batch" "11"   
[1] "Last Follow UP"
TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG 
         883           69           29          179          240         1094 
TCGA-PR-A5PH TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN 
         852          773          211           55           22          766 
TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RT-A6Y9 TCGA-RT-A6YA 
          70          134           24           29         2957         1249 
TCGA-RT-A6YC TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 
         246          604           89          216         1013          724 
TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D 
          32           26           37          356          191         2214 
TCGA-RW-A7D0 TCGA-SP-A6QD TCGA-SP-A6QH TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
          54         3087         1857         2983          274         3013 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MR TCGA-SR-A6MS TCGA-SR-A6MT 
          43            3         1558         2020         2222         3247 
TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
        3362         3269           NA          456          345         1106 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7HA 
         132          765          242          317          770           36 
TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A815 
         218          195          137          188           24          182 
TCGA-XG-A823 
         210 
Variable 1:'AGE':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=TRUE.
Variable 3:'DAYSTODEATH':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'BATCH.NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"    "GENDER" "RACE"  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 61 columns, 0 survival variables, and 3 non-survival variables.
AGE, nv=39, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, continuous
D1V2, binary
          cls
clus        0  1
  subtype1  3  1
  subtype2  2  5
  subtype3 19  2
  subtype4  9  9
  subtype5  4  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    1
  subtype2    2    5
  subtype3   19    2
  subtype4    9    9
  subtype5    4    3
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE        3        2       19        9        4
  MALE          1        5        2        9        3
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         0
  subtype2                                0     0                         1
  subtype3                                1     1                         3
  subtype4                                0     0                         3
  subtype5                                0     1                         0
          vv
clus       WHITE
  subtype1     3
  subtype2     6
  subtype3    15
  subtype4    15
  subtype5     6
D1V3, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1        0        0
  ASIAN                                   0        0        1        0        1
  BLACK OR AFRICAN AMERICAN               0        1        3        3        0
  WHITE                                   3        6       15       15        6
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, continuous
D2V2, binary
          cls
clus        0  1
  subtype1  7  7
  subtype2 22  6
  subtype3 11  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    7
  subtype2   22    6
  subtype3   11    8
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        7       22       11
  MALE          7        6        8
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                         1
  subtype2                                1     0                         5
  subtype3                                0     2                         1
          vv
clus       WHITE
  subtype1    11
  subtype2    21
  subtype3    16
D2V3, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                   1        0        2
  BLACK OR AFRICAN AMERICAN               1        5        1
  WHITE                                  11       21       16
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, continuous
D3V2, binary
          cls
clus        0  1
  subtype1 10  3
  subtype2 15  6
  subtype3  7 11
  subtype4  8  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    3
  subtype2   15    6
  subtype3    7   11
  subtype4    8    1
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       10       15        7        8
  MALE          3        6       11        1
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                         2
  subtype2                                1     0                         3
  subtype3                                0     1                         0
  subtype4                                0     1                         2
          vv
clus       WHITE
  subtype1     8
  subtype2    17
  subtype3    17
  subtype4     6
D3V3, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0
  ASIAN                                   1        0        1        1
  BLACK OR AFRICAN AMERICAN               2        3        0        2
  WHITE                                   8       17       17        6
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, continuous
D4V2, binary
          cls
clus        0  1
  subtype1  8  6
  subtype2 20  5
  subtype3  5  8
  subtype4  7  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    6
  subtype2   20    5
  subtype3    5    8
  subtype4    7    2
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        8       20        5        7
  MALE          6        5        8        2
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                         1
  subtype2                                1     0                         5
  subtype3                                0     1                         0
  subtype4                                0     1                         1
          vv
clus       WHITE
  subtype1    12
  subtype2    18
  subtype3    11
  subtype4     7
D4V3, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0
  ASIAN                                   1        0        1        1
  BLACK OR AFRICAN AMERICAN               1        5        0        1
  WHITE                                  12       18       11        7
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, continuous
D5V2, binary
          cls
clus        0  1
  subtype1 13 12
  subtype2 16  4
  subtype3 11  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   12
  subtype2   16    4
  subtype3   11    5
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       13       16       11
  MALE         12        4        5
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     2                         1
  subtype2                                0     0                         3
  subtype3                                0     1                         3
          vv
clus       WHITE
  subtype1    20
  subtype2    16
  subtype3    12
D5V3, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   2        0        1
  BLACK OR AFRICAN AMERICAN               1        3        3
  WHITE                                  20       16       12
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, continuous
D6V2, binary
          cls
clus        0  1
  subtype1 10 13
  subtype2 19  3
  subtype3  3  3
  subtype4  8  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10   13
  subtype2   19    3
  subtype3    3    3
  subtype4    8    2
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       10       19        3        8
  MALE         13        3        3        2
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     2                         1
  subtype2                                1     0                         3
  subtype3                                0     0                         1
  subtype4                                0     1                         2
          vv
clus       WHITE
  subtype1    19
  subtype2    17
  subtype3     5
  subtype4     7
D6V3, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0
  ASIAN                                   2        0        0        1
  BLACK OR AFRICAN AMERICAN               1        3        1        2
  WHITE                                  19       17        5        7
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MIRSEQ_MATURE_CNMF
D7V1, continuous
D7V2, binary
          cls
clus        0  1
  subtype1  8  6
  subtype2 19  5
  subtype3 13 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    6
  subtype2   19    5
  subtype3   13   10
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        8       19       13
  MALE          6        5       10
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                         0
  subtype2                                0     0                         5
  subtype3                                1     2                         2
          vv
clus       WHITE
  subtype1    12
  subtype2    18
  subtype3    18
D7V3, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1
  ASIAN                                   1        0        2
  BLACK OR AFRICAN AMERICAN               0        5        2
  WHITE                                  12       18       18
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D8V1, continuous
D8V2, binary
          cls
clus        0  1
  subtype1 11 13
  subtype2 18  3
  subtype3 11  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11   13
  subtype2   18    3
  subtype3   11    5
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       11       18       11
  MALE         13        3        5
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     2                         1
  subtype2                                1     0                         3
  subtype3                                0     1                         3
          vv
clus       WHITE
  subtype1    20
  subtype2    16
  subtype3    12
D8V3, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                   2        0        1
  BLACK OR AFRICAN AMERICAN               1        3        3
  WHITE                                  20       16       12
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
