Problems with FirebrowseR - query limit sizes

Question

[madraghrua1690]

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!

Answer 1

[Mdeng]

The problem is this exception

In addition: Warning message:
In download.Data(url, format, page) :
  The API responded with code  414. Your query might be to big

In this case, the API does not return any data. Hence, mRNA.Exp remains empty and accessing it with mRNA.Exp[[page.Counter]] gives you an out of bounds exception. Anyway, the code above is (currently) working for me. The API is not that reliable, maybe try using only one or two genes at a time or lower the amount of patients (barcodes) per API request.