
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/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/LUSC-TP/3471934/0.miRseq_preprocessor.Finished/LUSC-TP.miRseq_RPKM_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/LUSC-TP/3351655/LUSC-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=351, in expression file=369, common to both=314
Number of genes in original expression dataset=542
[1] "ALL"
[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] "COMPLETENESS.OF.RESECTION"             
[18] "TUMOR.STAGECODE"                       
[19] "NEOPLASM.DISEASESTAGE"                 
[20] "BATCHNUMBER"                           

Input Data has 20 rows and 314 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 
         370          136         2466          146         1415          345 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
         396         1810          862          758           49         1331 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1072 TCGA-21-1075 
          85         2753           92          826         3016         2133 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1083 
        1852         1058          473          964         3724          267 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 
         962           NA          908          661          329          608 
TCGA-22-0944 TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
         223           53          429          622         1067         1470 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
         734           17         1057          399           NA          587 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
          NA          358          964         1974         1932          444 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 
        1345           24         1651         2170           NA          357 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 
         573          915         1912         1713          505         2524 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
        3469         2979         1311         5286         3149         4299 
TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-34-2596 
         428           NA          334           NA          821           80 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 
        1874          958          881          999          950         1528 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
        1575          994           NA          329          235          428 
TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-37-3783 TCGA-37-3789 
         698          168           NA           NA          120           13 
TCGA-37-3792 TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
          12          246          238          207           12          103 
TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
        1454         1360         2086           NA         2130         1848 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 
          52          740           59          832         1107          474 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 
        1084           24          544           NA          556          550 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 
         399          352          267          258          549          213 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 
         183           85           NA           NA          212           48 
TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 
        2023          202          193           NA           NA           NA 
TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
          NA           NA           29           18           12           12 
TCGA-51-4081 TCGA-51-6867 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 
          63           NA          541           NA          922           NA 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 
          NA          880            3           NA           62           31 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 
          30           13           30           44           40           26 
TCGA-56-7730 TCGA-56-7822 TCGA-56-8504 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 
           6            1          177           36           17           16 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-60-2695 
          34           30           NA           46           30          473 
TCGA-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 
         109           NA          311           NA           NA         2500 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 
        2082         1505         1685          888          274         1456 
TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 
         512         1181          931           96          793          733 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-5128 TCGA-63-5131 TCGA-63-6202 
         693           37          719           NA           NA           NA 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 
          NA           NA           NA           NA         1311           61 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2758 
         641           30           31           61           28          638 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
         761           30           61           31           61           61 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
         700          578           61           NA          121           NA 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 
         759           59          790         1217          699           NA 
TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 
         699           NA          913           NA         1645          122 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
        1492           83          202          211          244           95 
TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
          NA           NA           NA           NA           NA           NA 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
          NA         2736           NA           15         1285           NA 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 
          NA           NA           NA          479           NA           NA 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
        1641           NA         2522           NA           NA           NA 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 
          NA         3166           NA           NA          833           NA 
TCGA-77-8146 TCGA-77-8148 TCGA-77-8150 TCGA-77-8154 TCGA-77-8156 TCGA-79-5596 
        2183          293           NA         1092           10           NA 
TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 
          NA           11           24           34           18           10 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 
          49            1           NA           35           38           60 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 
          26           60           16           43           14           36 
TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 
          13           44           54           41           47           89 
TCGA-90-7769 TCGA-90-7964 TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 
          18          100           82          106          122          160 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-96-7544 TCGA-96-7545 
          69           87           NA          143         1213         1323 
TCGA-96-8169 TCGA-96-8170 TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
         188          210          115          413          223          308 
TCGA-J1-A4AH TCGA-L3-A4E7 
         222           35 
Variable 1:'AGE':	nDistinctValues=43,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=107,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=204,	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=19,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=115,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'HISTOLOGICAL.TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'NUMBERPACKYEARSSMOKED':	nDistinctValues=84,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=48,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'DISTANT.METASTASIS':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'LYMPH.NODE.METASTASIS':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'TUMOR.STAGECODE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NEOPLASM.DISEASESTAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=17,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "GENDER"                                
 [3] "KARNOFSKY.PERFORMANCE.SCORE"           
 [4] "HISTOLOGICAL.TYPE"                     
 [5] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [6] "NUMBERPACKYEARSSMOKED"                 
 [7] "YEAROFTOBACCOSMOKINGONSET"             
 [8] "DISTANT.METASTASIS"                    
 [9] "LYMPH.NODE.METASTASIS"                 
[10] "COMPLETENESS.OF.RESECTION"             
[11] "TUMOR.STAGECODE"                       
[12] "NEOPLASM.DISEASESTAGE"                 
[1] "TUMOR.?STAGE" "11"          
[1] "stage2"
vv
 T1 T1A T1B  T2 T2A T2B  T3  T4 
 36  13  25 135  40  16  33  16 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 314 columns, 1 survival variables, and 12 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
HSA-MIR-125B-2 
            45 
AGE, nv=43, binary=FALSE, numeric=TRUE
HSA-MIR-99A 
        541 
GENDER, nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-375 
        325 
KARNOFSKY.PERFORMANCE.SCORE, nv=8, binary=FALSE, numeric=TRUE
HSA-MIR-499 
        393 
HISTOLOGICAL.TYPE, nv=4, binary=FALSE, numeric=FALSE
HSA-MIR-29A 
        204 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-383 
        337 
NUMBERPACKYEARSSMOKED, nv=84, binary=FALSE, numeric=TRUE
HSA-MIR-147B 
          99 
YEAROFTOBACCOSMOKINGONSET, nv=48, binary=FALSE, numeric=TRUE
HSA-MIR-337 
        270 
DISTANT.METASTASIS, nv=3, binary=FALSE, numeric=FALSE
HSA-MIR-26A-1 
          196 
LYMPH.NODE.METASTASIS, nv=5, binary=FALSE, numeric=FALSE
HSA-MIR-641 
        486 
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
HSA-MIR-3607 
         282 
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
[1] "Clinical variable TUMOR.STAGECODE has too few non-missing values, n=0"
NEOPLASM.DISEASESTAGE, nv=9, binary=FALSE, numeric=FALSE
HSA-MIR-361 
        284 
> q(save="no")
