Hi all,

I have downloaded the TCGA-BRCA RNA-seq data and the associated clinical information using the code below.

CancerProject <- "TCGA-BRCA"

query <- GDCquery(project = CancerProject,
                  data.category = "Transcriptome Profiling",
                  data.type = "Gene Expression Quantification", 
                  workflow.type = "HTSeq - Counts")

samplesDown <- getResults(query,cols=c("cases"))

dataSmTP <- TCGAquery_SampleTypes(barcode = samplesDown,
                                  typesample = "TP")

queryDown <- GDCquery(project = CancerProject, 
                      data.category = "Transcriptome Profiling",
                      data.type = "Gene Expression Quantification", 
                      workflow.type = "HTSeq - Counts", 
                      barcode = dataSmTP)

GDCdownload(query = queryDown,directory = "BRC_RESULTS/TCGA/htseq_data/")                    

dataPrep <- GDCprepare(query = queryDown, 
                       save = TRUE, 
                       directory =  "BRC_RESULTS/TCGA/htseq_data/",
                       save.filename = "htseq_counts.rda", summarizedExperiment = TRUE)

In the clinical data there are several columns such as days_to_death or days_to_last_follow_up and other columns such as subtype_OS.Time or subtype_OS.event.

What is the difference between the columns having subtype_ at the begging and the rest and which one should I use for survival analysis? At the moment I have used the subtype_ columns for my analysis and I am wondering if this correct.

Thanks a lot,

Matina