
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/mRNAseq_preprocessor/LAML/1676709/0.mRNAseq_preprocessor.Finished/LAML.mRNAseq_RPKM_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LAML/1669663/1.GDAC_clinicalDataPicker.Finished/LAML.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=200, in expression file=179, common to both=179
Number of genes in original expression dataset=17799
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                     "DAYSTODEATH"                     
 [3] "DAYSTOLASTFOLLOWUP"               "VITALSTATUS"                     
 [5] "DCCUPLOADDATE"                    "PRIMARYSITEOFDESEASE"            
 [7] "GENDER"                           "DATEOFINITIALPATHOLOGICDIAGNOSIS"
 [9] "DAYSTOLASTKNOWNALIVE"             "KARNOFSKYPERFORMANCESCORE"       
[11] "BATCHNUMBER"                     

Input Data has 11 rows and 179 columns.

[1] "Batch" "11"   
[1] "Last Follow UP"
TCGA-AB-2803 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 TCGA-AB-2810 
          NA           NA           NA           NA         2861           NA 
TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 TCGA-AB-2815 TCGA-AB-2816 
          NA           NA           NA           NA           NA           NA 
TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 TCGA-AB-2822 
          NA           NA         2496           NA           NA           NA 
TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2828 TCGA-AB-2830 
          NA           NA           NA           NA         2284           NA 
TCGA-AB-2832 TCGA-AB-2833 TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 
          NA           NA           NA         1673           NA           NA 
TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2843 
          NA           NA           NA           NA           NA           NA 
TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2847 TCGA-AB-2848 TCGA-AB-2849 
          NA           NA           NA           NA           NA         2220 
TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2856 TCGA-AB-2857 
          NA           NA           NA           NA           NA           NA 
TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 
          NA           NA           NA           NA         1430           NA 
TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 
          NA           NA           NA           NA          243           NA 
TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2876 
         153          638          273          396          212         1219 
TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2880 TCGA-AB-2881 TCGA-AB-2882 
         638           NA          245          424          393           NA 
TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2887 TCGA-AB-2888 
         730           NA           NA          181           NA          334 
TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2891 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 
         304           NA           NA          942           NA           NA 
TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 
          NA           NA          243          393           NA           NA 
TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 
          58           NA           NA           NA           30           NA 
TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 
        1186           NA         1216          792           NA          882 
TCGA-AB-2917 TCGA-AB-2918 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2921 TCGA-AB-2924 
        1216           NA           61           NA           NA           90 
TCGA-AB-2925 TCGA-AB-2927 TCGA-AB-2928 TCGA-AB-2929 TCGA-AB-2930 TCGA-AB-2931 
          NA           NA           59           NA           NA           NA 
TCGA-AB-2932 TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 
          NA           NA           28           NA           59           NA 
TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2940 TCGA-AB-2941 TCGA-AB-2942 TCGA-AB-2943 
          NA          455           NA           NA          641           NA 
TCGA-AB-2944 TCGA-AB-2946 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 
          NA           NA           NA          699          306           NA 
TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 
        1492           NA           NA           NA           NA         1277 
TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 
          NA           NA         1035         1127           NA           NA 
TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2975 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 
          NA           NA           NA           NA           NA          699 
TCGA-AB-2979 TCGA-AB-2980 TCGA-AB-2981 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 
         671          699          487          149           NA         1156 
TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2990 TCGA-AB-2991 
          NA           NA           NA           NA          457         1826 
TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 
          NA           NA         1798         1551         1581           NA 
TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 
        1734         1249         1581           NA         2099           NA 
TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
        1581           NA           NA         1885         1887 
Variable 1:'AGE':	nDistinctValues=61,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=62,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=54,	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=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'BATCH.NUMBER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"    "GENDER"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 179 columns, 1 survival variables, and 2 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
IL2RA|3559_CALCULATED 
                 2169 
AGE, nv=61, binary=FALSE, numeric=TRUE
GBP2|2634_CALCULATED 
                 645 
GENDER, nv=2, binary=FALSE, numeric=FALSE
DDX3Y|8653_CALCULATED 
                17782 
> q(save="no")
