
R version 2.10.1 (2009-12-14)
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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/ClinicalAnalysisAllGenes_new.13.3873/ClinicalAnalysisAllGenes.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ClinicalAnalysisAllGenes_new.13.3873/", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/miRseq_preprocessor/SKCM-TM/2859940/0.miRseq_preprocessor.Finished/SKCM-TM.miRseq_RPKM_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/SKCM-TM/2844285/1.GDAC_clinicalDataPicker.Finished/SKCM-TM.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=165, in expression file=235, common to both=154
Number of genes in original expression dataset=615
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "GENDER"                                
 [7] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [8] "RADIATIONTHERAPY"                      
 [9] "RADIATIONS.RADIATION.REGIMENINDICATION"
[10] "DISTANT.METASTASIS"                    
[11] "LYMPH.NODE.METASTASIS"                 
[12] "TUMOR.STAGECODE"                       
[13] "NEOPLASM.DISEASESTAGE"                 
[14] "BATCHNUMBER"                           

Input Data has 14 rows and 154 columns.

[1] "Batch" "14"   
[1] "Last Follow UP"
TCGA-D3-A1Q7 TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A148 
        3687           NA         2167           NA          653         4511 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV 
        1513           82          194          345           98         1487 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
          NA         3564           NA         5926           NA           NA 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
        3265         1861           NA           NA          713           NA 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z 
         870           NA         6553          477           NA           NA 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
          NA           NA           NA           NA         3335         2399 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
          NA           NA         1455           NA         1205          979 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
          NA         1349           NA         1716         1136          440 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        1700        10523           NA           NA           NA         2401 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
         743           NA         1787         1446         1315         9567 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
        4134         5536          686         2717         1664         1673 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
        2296         2766         3101           NA          435         1691 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
         595         2042           NA         3931           NA           NA 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
          NA         4403         6175           NA           NA         7562 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
          NA         3150         4150         1265         1620          129 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
        3733          786          112          813           NA          714 
TCGA-EE-A3AH TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
          NA           NA           NA           NA           NA           NA 
TCGA-ER-A19N TCGA-ER-A19O TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN 
        1340           NA         2433         2443         1010         2448 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
          NA           NA           NA           NA           NA         1225 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
          NA           NA           NA           NA           NA         3080 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
          NA           NA           NA         4525         1617           NA 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
        1505           NA           NA            6          699         1446 
TCGA-FW-A3TV TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
          NA           NA         3664           NA         2577           NA 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
          NA           NA           NA         1204 
Variable 1:'AGE':	nDistinctValues=61,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=72,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=78,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=26,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 8:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'DISTANT.METASTASIS':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'LYMPH.NODE.METASTASIS':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'TUMOR.STAGECODE':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'NEOPLASM.DISEASESTAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'BATCH.NUMBER':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                   "GENDER"                "DISTANT.METASTASIS"   
[4] "LYMPH.NODE.METASTASIS" "TUMOR.STAGECODE"       "NEOPLASM.DISEASESTAGE"
[1] "TUMOR.?STAGE" "5"           
[1] "stage2"
vv
 T0  T1 T1A T1B  T2 T2A T2B  T3 T3A T3B  T4 T4A T4B TIS  TX 
  4   4  13   2  17  15   6   4  20  12   4   6  20   1   9 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 154 columns, 1 survival variables, and 6 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
HSA-MIR-155 
        124 
AGE, nv=61, binary=FALSE, numeric=TRUE
HSA-MIR-3680 
         351 
GENDER, nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-361 
        323 
DISTANT.METASTASIS, nv=5, binary=FALSE, numeric=FALSE
HSA-MIR-3654 
         341 
LYMPH.NODE.METASTASIS, nv=10, binary=FALSE, numeric=FALSE
HSA-MIR-185 
        139 
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
[1] "Clinical variable TUMOR.STAGECODE has too few non-missing values, n=0"
NEOPLASM.DISEASESTAGE, nv=12, binary=FALSE, numeric=FALSE
HSA-MIR-199A-1 
           166 
> q(save="no")
