[1] "R version 2.15.3 (2013-03-01)"
[1] "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "dx" ""  
[1] "dx" " " 
[1] "dx" " " 
[1] "opt:  RPPA_EXPR"
[1] "vtyp==survival in table1 generation"
[1] "vtyp==survival in table1 generation"
[1] "vtyp==continuous in table1 table generation"
[1] "vtyp==multiclass in table1 generation"
[1] "vtyp==multiclass in table1 generation"
[1] "vtyp==continuous in table1 table generation"
[1] "vtyp==continuous in table1 table generation"
[1] "vtyp==binary in table1 table generation"
[1] "vtyp==binary in table1 table generation"
[1] "vtyp==binary in table1 table generation"
[1] "vtyp==continuous in table1 table generation"
[1] "vtyp==binary in table1 table generation"
                                           Clinical feature                            
TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
DAYS_TO_DEATH_OR_LAST_FUP                  "DAYS_TO_DEATH_OR_LAST_FUP"                 
YEARS_TO_BIRTH                             "YEARS_TO_BIRTH"                            
PRIMARY_SITE_OF_DISEASE                    "PRIMARY_SITE_OF_DISEASE"                   
NEOPLASM_DISEASESTAGE                      "NEOPLASM_DISEASESTAGE"                     
PATHOLOGY_T_STAGE                          "PATHOLOGY_T_STAGE"                         
PATHOLOGY_N_STAGE                          "PATHOLOGY_N_STAGE"                         
PATHOLOGY_M_STAGE                          "PATHOLOGY_M_STAGE"                         
MELANOMA_ULCERATION                        "MELANOMA_ULCERATION"                       
MELANOMA_PRIMARY_KNOWN                     "MELANOMA_PRIMARY_KNOWN"                    
BRESLOW_THICKNESS                          "BRESLOW_THICKNESS"                         
GENDER                                     "GENDER"                                    
                                           Statistical test           
TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP "Cox regression test"      
DAYS_TO_DEATH_OR_LAST_FUP                  "Cox regression test"      
YEARS_TO_BIRTH                             "Spearman correlation test"
PRIMARY_SITE_OF_DISEASE                    "Kruskal-Wallis test"      
NEOPLASM_DISEASESTAGE                      "Kruskal-Wallis test"      
PATHOLOGY_T_STAGE                          "Spearman correlation test"
PATHOLOGY_N_STAGE                          "Spearman correlation test"
PATHOLOGY_M_STAGE                          "Wilcoxon test"            
MELANOMA_ULCERATION                        "Wilcoxon test"            
MELANOMA_PRIMARY_KNOWN                     "Wilcoxon test"            
BRESLOW_THICKNESS                          "Spearman correlation test"
GENDER                                     "Wilcoxon test"            
                                           Significant genes
TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP "N=20"           
DAYS_TO_DEATH_OR_LAST_FUP                  "N=30"           
YEARS_TO_BIRTH                             "N=12"           
PRIMARY_SITE_OF_DISEASE                    "N=30"           
NEOPLASM_DISEASESTAGE                      "N=0"            
PATHOLOGY_T_STAGE                          "N=0"            
PATHOLOGY_N_STAGE                          "N=5"            
PATHOLOGY_M_STAGE                          "N=0"            
MELANOMA_ULCERATION                        "N=0"            
MELANOMA_PRIMARY_KNOWN                     "N=15"           
BRESLOW_THICKNESS                          "N=30"           
GENDER                                     "N=0"            
                                           Associated with           
TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP "shorter survival"        
DAYS_TO_DEATH_OR_LAST_FUP                  "shorter survival"        
YEARS_TO_BIRTH                             "older"                   
PRIMARY_SITE_OF_DISEASE                    " "                       
NEOPLASM_DISEASESTAGE                      " "                       
PATHOLOGY_T_STAGE                          " "                       
PATHOLOGY_N_STAGE                          "higher stage"            
PATHOLOGY_M_STAGE                          " "                       
MELANOMA_ULCERATION                        " "                       
MELANOMA_PRIMARY_KNOWN                     "yes"                     
BRESLOW_THICKNESS                          "higher breslow_thickness"
GENDER                                     " "                       
                                           &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP "N=7"                                                                                     
DAYS_TO_DEATH_OR_LAST_FUP                  "N=15"                                                                                    
YEARS_TO_BIRTH                             "N=4"                                                                                     
PRIMARY_SITE_OF_DISEASE                    " "                                                                                       
NEOPLASM_DISEASESTAGE                      " "                                                                                       
PATHOLOGY_T_STAGE                          " "                                                                                       
PATHOLOGY_N_STAGE                          "N=4"                                                                                     
PATHOLOGY_M_STAGE                          " "                                                                                       
MELANOMA_ULCERATION                        " "                                                                                       
MELANOMA_PRIMARY_KNOWN                     "N=15"                                                                                    
BRESLOW_THICKNESS                          "N=13"                                                                                    
GENDER                                     " "                                                                                       
                                           Associated with                 
TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP "longer survival"         "N=13"
DAYS_TO_DEATH_OR_LAST_FUP                  "longer survival"         "N=15"
YEARS_TO_BIRTH                             "younger"                 "N=8" 
PRIMARY_SITE_OF_DISEASE                    " "                       " "   
NEOPLASM_DISEASESTAGE                      " "                       " "   
PATHOLOGY_T_STAGE                          " "                       " "   
PATHOLOGY_N_STAGE                          "lower stage"             "N=1" 
PATHOLOGY_M_STAGE                          " "                       " "   
MELANOMA_ULCERATION                        " "                       " "   
MELANOMA_PRIMARY_KNOWN                     "no"                      "N=0" 
BRESLOW_THICKNESS                          "lower breslow_thickness" "N=17"
GENDER                                     " "                       " "   
[1] "vtyp==survival in basici table generation"
[1] "check. how many intervals of data quantile for survival curve?"
[1] 4
[1] "check. how many intervals of data quantile for survival curve?"
[1] 4
[1] "check. how many intervals of data quantile for survival curve?"
[1] 4
[1] "check. how many intervals of data quantile for survival curve?"
[1] 4
[1] "check. how many intervals of data quantile for survival curve?"
[1] 4
[1] "check. how many intervals of data quantile for survival curve?"
[1] 4
[1] "check. how many intervals of data quantile for survival curve?"
[1] 4
[1] "check. how many intervals of data quantile for survival curve?"
[1] 4
[1] "check. how many intervals of data quantile for survival curve?"
[1] 4
[1] "check. how many intervals of data quantile for survival curve?"
[1] 4
[1] "vtyp==survival in basici table generation"
[1] "check. how many intervals of data quantile for survival curve?"
[1] 4
[1] "check. how many intervals of data quantile for survival curve?"
[1] 4
[1] "check. how many intervals of data quantile for survival curve?"
[1] 4
[1] "check. how many intervals of data quantile for survival curve?"
[1] 4
[1] "check. how many intervals of data quantile for survival curve?"
[1] 4
[1] "check. how many intervals of data quantile for survival curve?"
[1] 4
[1] "check. how many intervals of data quantile for survival curve?"
[1] 4
[1] "check. how many intervals of data quantile for survival curve?"
[1] 4
[1] "check. how many intervals of data quantile for survival curve?"
[1] 4
[1] "check. how many intervals of data quantile for survival curve?"
[1] 4
[1] "vtyp==continuous in basici table generation"
[1] "vtyp==multiclass in basici table generation"
[1] "vtyp==multiclass in basici table generation"
[1] "vtyp==continuous in basici table generation"
[1] "vtyp==continuous in basici table generation"
[1] "vtyp==binary in basici table generation"
[1] "vtyp==binary in basici table generation"
[1] "vtyp==binary in basici table generation"
[1] "vtyp==continuous in basici table generation"
[1] "vtyp==binary in basici table generation"
