
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/GDAC_RPPA_preprocess/COADREAD-TP/3353098/0.GDAC_RPPA_preprocess.Finished/COADREAD-TP.rppa.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/COADREAD-TP/3350932/COADREAD-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=1182, in expression file=461, common to both=461
Number of genes in original expression dataset=171
[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] "HISTOLOGICALTYPE"                      
[11] "RADIATIONS.RADIATION.REGIMENINDICATION"
[12] "DISTANT.METASTASIS"                    
[13] "LYMPH.NODE.METASTASIS"                 
[14] "COMPLETENESS.OF.RESECTION"             
[15] "NUMBER.OF.LYMPH.NODES"                 
[16] "TUMOR.STAGECODE"                       
[17] "NEOPLASM.DISEASESTAGE"                 
[18] "BATCHNUMBER"                           

Input Data has 18 rows and 461 columns.

[1] "Batch" "18"   
[1] "Last Follow UP"
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 
         648          503          447          541          437          522 
TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
         552          472          387          464          488          332 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
         278          313          246          462          367          286 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
         342          306          297          362          286          244 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
         320          195          181          124          129          133 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
         253          146          172          248          134           90 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
         177           86          158          164           31           NA 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
          31           31           NA           31           NA           NA 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3521 TCGA-AA-3522 TCGA-AA-3525 
          NA           NA           NA           NA           NA           NA 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3548 
          NA           NA           NA           NA           NA           NA 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 
          NA           NA           NA           30           NA           NA 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3678 
          NA           31           NA           NA           NA           NA 
TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3695 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
          NA           NA           NA           NA           29           31 
TCGA-AA-3712 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3814 
          NA           29           30           30           NA           NA 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
          NA           NA           NA           NA           NA           31 
TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 
          NA           28           NA           30           NA           NA 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3861 TCGA-AA-3862 TCGA-AA-3864 TCGA-AA-3866 
          31           30           NA           31           NA           NA 
TCGA-AA-3869 TCGA-AA-3872 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3955 
          NA           NA           NA           30           31           NA 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 
          NA           NA           NA           NA           30           NA 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F 
          30           NA          424          548          913         1035 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R 
         548          548          517           NA          822           30 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
         517          456          669          638          457          457 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
          30          396          365          396           NA           31 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A022 
        1065           31         1005         1065          791           NA 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
          NA         1580           NA         1215           NA           NA 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
          NA           28           NA         1246         1215           NA 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6965 
        1245            2            3         1719           47            6 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
          14           28          203          230            6          112 
TCGA-AY-6386 TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
         168         1714         1334           NA           NA          505 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
          NA           NA         1705         1395           NA           NA 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
          NA           NA           NA           NA           NA           NA 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
          NA            5            2           NA           12            8 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-5914 
           2            8           10            3           41          669 
TCGA-CK-5916 TCGA-CK-6746 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
          NA           NA           89           61         3134          184 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4752 
         214          699          244          214          244          123 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
         183          304          393          335          304          335 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
          NA          304           61          304          212          212 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
          90          487          212          424          122          181 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
         243          242          181          211          149          152 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 
         152          152          122          122           91          204 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
          30          198          202          260          271           17 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
         107           40          241           10          287          136 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
         246          144          186          108           45          111 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
         133           42           88           95           67           20 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 
          45           43           19         3429         1162         3621 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
        2821         1518           NA          383         3927          227 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
        1348         3927         3774          235         4122          426 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28M 
         805         2475         3529         1094         1849         2774 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
          NA           NA           NA           NA           NA           NA 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
          56           46           16           20           16           14 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
          38           16           42           20         3203           NA 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
         254         2288           NA         2077         1309         1882 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
        1631         1358         1485         1386         1204         1112 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
        1031          937          893          678          571          546 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 
         201          741          644         2672           NA         1434 
TCGA-G4-6628 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-3914 
        1611          482          358          387          316          264 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3578 
         257          231          193          223           NA           NA 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
          NA           31           31           61           NA           31 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
          31           NA           NA           NA           NA           30 
TCGA-AG-3600 TCGA-AG-3601 TCGA-AG-3602 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 
          NA           NA           NA           30           NA           NA 
TCGA-AG-3725 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
          NA           29           31           30           30           NA 
TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3891 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 
          NA           NA           30           30           31           NA 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
          NA           NA           31           NA           31           31 
TCGA-AG-4015 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
          NA           NA           30          637          423          183 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
         789          700          518          484          396           31 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
          31          365         2130         1946          334           NA 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A036 TCGA-AH-6544 
          NA           NA         1884         1246         2192           15 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 
          44            6           21           22          140          310 
TCGA-CI-6621 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
          NA          243          334          335          304          153 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
         224          212          849          212          608          180 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
         121          152            8         3635         1257         1741 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
        3683          734         1566          991           15           73 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
         232            5           66          250           14          121 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 
          20          210          216          187          108           83 
TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
         159          237           NA          103           26           66 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 
          12           31           20           21           33           23 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
          14           NA         1451           NA          636 
Variable 1:'AGE':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=50,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=227,	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=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=24,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DISTANT.METASTASIS':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'TUMOR.STAGECODE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NEOPLASM.DISEASESTAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'BATCH.NUMBER':	nDistinctValues=25,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "PRIMARY.SITE.OF.DISEASE"               
 [3] "GENDER"                                
 [4] "HISTOLOGICAL.TYPE"                     
 [5] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [6] "DISTANT.METASTASIS"                    
 [7] "LYMPH.NODE.METASTASIS"                 
 [8] "COMPLETENESS.OF.RESECTION"             
 [9] "NUMBER.OF.LYMPH.NODES"                 
[10] "TUMOR.STAGECODE"                       
[11] "NEOPLASM.DISEASESTAGE"                 
[1] "TUMOR.?STAGE" "10"          
[1] "stage2"
vv
 T0  T1  T2  T3  T4 T4A T4B TIS 
  1  10  76 324  24  17   7   1 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 461 columns, 1 survival variables, and 11 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
PARP1|PARP_CLEAVED-M-C 
                    98 
AGE, nv=59, binary=FALSE, numeric=TRUE
MAP2K1|MEK1_PS217_S221-R-V 
                        87 
PRIMARY.SITE.OF.DISEASE, nv=2, binary=FALSE, numeric=FALSE
CHEK1|CHK1_PS345-R-C 
                  41 
GENDER, nv=2, binary=FALSE, numeric=FALSE
AKT1AKT2 AKT3|AKT_PS473-R-V 
                         16 
HISTOLOGICAL.TYPE, nv=4, binary=FALSE, numeric=FALSE
CHEK1|CHK1_PS345-R-C 
                  41 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
PECAM1|CD31-M-V 
             31 
DISTANT.METASTASIS, nv=5, binary=FALSE, numeric=FALSE
IGFBP2|IGFBP2-R-V 
               76 
LYMPH.NODE.METASTASIS, nv=9, binary=FALSE, numeric=FALSE
EIF4E|EIF4E-R-V 
            158 
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
PIK3CA|PI3K-P110-ALPHA-R-C 
                       102 
NUMBER.OF.LYMPH.NODES, nv=27, binary=FALSE, numeric=TRUE
IRS1|IRS1-R-V 
           78 
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
[1] "Clinical variable TUMOR.STAGECODE has too few non-missing values, n=0"
NEOPLASM.DISEASESTAGE, nv=13, binary=FALSE, numeric=FALSE
PIK3CA|PI3K-P110-ALPHA-R-C 
                       102 
> q(save="no")
