[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==continuous in table1 table 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==continuous in table1 table generation"
[1] "vtyp==continuous in table1 table generation"
[1] "vtyp==continuous in table1 table generation"
[1] "vtyp==multiclass in table1 generation"
[1] "vtyp==binary in table1 table generation"
                                       Clinical feature                        
DAYS_TO_DEATH_OR_LAST_FUP              "DAYS_TO_DEATH_OR_LAST_FUP"             
YEARS_TO_BIRTH                         "YEARS_TO_BIRTH"                        
NEOPLASM_DISEASESTAGE                  "NEOPLASM_DISEASESTAGE"                 
PATHOLOGY_T_STAGE                      "PATHOLOGY_T_STAGE"                     
PATHOLOGY_N_STAGE                      "PATHOLOGY_N_STAGE"                     
GENDER                                 "GENDER"                                
RADIATIONS_RADIATION_REGIMENINDICATION "RADIATIONS_RADIATION_REGIMENINDICATION"
NUMBER_PACK_YEARS_SMOKED               "NUMBER_PACK_YEARS_SMOKED"              
YEAR_OF_TOBACCO_SMOKING_ONSET          "YEAR_OF_TOBACCO_SMOKING_ONSET"         
NUMBER_OF_LYMPH_NODES                  "NUMBER_OF_LYMPH_NODES"                 
RACE                                   "RACE"                                  
ETHNICITY                              "ETHNICITY"                             
                                       Statistical test           
DAYS_TO_DEATH_OR_LAST_FUP              "Cox regression test"      
YEARS_TO_BIRTH                         "Spearman correlation test"
NEOPLASM_DISEASESTAGE                  "Kruskal-Wallis test"      
PATHOLOGY_T_STAGE                      "Spearman correlation test"
PATHOLOGY_N_STAGE                      "Spearman correlation test"
GENDER                                 "Wilcoxon test"            
RADIATIONS_RADIATION_REGIMENINDICATION "Wilcoxon test"            
NUMBER_PACK_YEARS_SMOKED               "Spearman correlation test"
YEAR_OF_TOBACCO_SMOKING_ONSET          "Spearman correlation test"
NUMBER_OF_LYMPH_NODES                  "Spearman correlation test"
RACE                                   "Kruskal-Wallis test"      
ETHNICITY                              "Wilcoxon test"            
                                       Significant genes
DAYS_TO_DEATH_OR_LAST_FUP              "N=2"            
YEARS_TO_BIRTH                         "N=0"            
NEOPLASM_DISEASESTAGE                  "N=26"           
PATHOLOGY_T_STAGE                      "N=30"           
PATHOLOGY_N_STAGE                      "N=30"           
GENDER                                 "N=28"           
RADIATIONS_RADIATION_REGIMENINDICATION "N=29"           
NUMBER_PACK_YEARS_SMOKED               "N=4"            
YEAR_OF_TOBACCO_SMOKING_ONSET          "N=0"            
NUMBER_OF_LYMPH_NODES                  "N=30"           
RACE                                   "N=2"            
ETHNICITY                              "N=0"            
                                       Associated with                  
DAYS_TO_DEATH_OR_LAST_FUP              "shorter survival"               
YEARS_TO_BIRTH                         " "                              
NEOPLASM_DISEASESTAGE                  " "                              
PATHOLOGY_T_STAGE                      "higher stage"                   
PATHOLOGY_N_STAGE                      "higher stage"                   
GENDER                                 "male"                           
RADIATIONS_RADIATION_REGIMENINDICATION "yes"                            
NUMBER_PACK_YEARS_SMOKED               "higher number_pack_years_smoked"
YEAR_OF_TOBACCO_SMOKING_ONSET          " "                              
NUMBER_OF_LYMPH_NODES                  "higher number_of_lymph_nodes"   
RACE                                   " "                              
ETHNICITY                              " "                              
                                       &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
DAYS_TO_DEATH_OR_LAST_FUP              "N=2"                                                                                     
YEARS_TO_BIRTH                         " "                                                                                       
NEOPLASM_DISEASESTAGE                  " "                                                                                       
PATHOLOGY_T_STAGE                      "N=17"                                                                                    
PATHOLOGY_N_STAGE                      "N=17"                                                                                    
GENDER                                 "N=28"                                                                                    
RADIATIONS_RADIATION_REGIMENINDICATION "N=29"                                                                                    
NUMBER_PACK_YEARS_SMOKED               "N=4"                                                                                     
YEAR_OF_TOBACCO_SMOKING_ONSET          " "                                                                                       
NUMBER_OF_LYMPH_NODES                  "N=14"                                                                                    
RACE                                   " "                                                                                       
ETHNICITY                              " "                                                                                       
                                       Associated with                        
DAYS_TO_DEATH_OR_LAST_FUP              "longer survival"                "N=0" 
YEARS_TO_BIRTH                         " "                              " "   
NEOPLASM_DISEASESTAGE                  " "                              " "   
PATHOLOGY_T_STAGE                      "lower stage"                    "N=13"
PATHOLOGY_N_STAGE                      "lower stage"                    "N=13"
GENDER                                 "female"                         "N=0" 
RADIATIONS_RADIATION_REGIMENINDICATION "no"                             "N=0" 
NUMBER_PACK_YEARS_SMOKED               "lower number_pack_years_smoked" "N=0" 
YEAR_OF_TOBACCO_SMOKING_ONSET          " "                              " "   
NUMBER_OF_LYMPH_NODES                  "lower number_of_lymph_nodes"    "N=16"
RACE                                   " "                              " "   
ETHNICITY                              " "                              " "   
[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] "vtyp==continuous 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==continuous in basici table generation"
[1] "vtyp==continuous in basici table generation"
[1] "vtyp==continuous in basici table generation"
[1] "vtyp==multiclass in basici table generation"
[1] "vtyp==binary in basici table generation"
