Hi Folks I'm a FirebrowseR newbie. I'm working through the tutorial for FireBrowseR from the Broad Institute. Through a set of manipulations I want to now retrieve data on about 152 patient samples.

Based on the tutorial I'm using the following code:

diff.Exp.Genes = c("ESR1", "GATA3", "XBP1", "FOXA1", "ERBB2", "GRB7", "EGFR", "FOXC1", "MYC")
all.Found = F
page.Counter = 1
mRNA.Exp = list()
page.Size = 2000 # using a bigger page size is faster
while(all.Found == F){
  mRNA.Exp[[page.Counter]] = Samples.mRNASeq(format = "csv",
                                             gene = diff.Exp.Genes,
                                             cohort = "BRCA",
                                             tcga_participant_barcode = brca.Pats$tcga_participant_barcode,
                                             page_size = page.Size,
                                             page = page.Counter)
  if(nrow(mRNA.Exp[[page.Counter]]) < page.Size)
    all.Found = T
  else
    page.Counter = page.Counter + 1
}
mRNA.Exp = do.call(rbind, mRNA.Exp)
dim(mRNA.Exp)

I'm getting the following as I run the code:

> source('~/Rscripts/RanchoBiotech/getDifferentialExpressedGenes.R')
Error in mRNA.Exp[[page.Counter]] : subscript out of bounds
In addition: Warning message:
In download.Data(url, format, page) :
  The API responded with code  414. Your query might be to big

I've tried a few things, reduce the numbers of genes, page sizes and so on. Has anyone else had a problem running the tutorial? Any suggestions on how to modify the tutorial to get these patient samples data sets back?

Thanks!