mRNA.Exp[[page.Counter]] : subscript out of bounds

Question

[j11patel]

i am trying to download mRNA expression for selected gene using tutorial available at below location https://github.com/mariodeng/FirebrowseR/blob/master/vignettes/FirebrowseR.Rmd

But, it is giving me an error:

"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"

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)

Please let me know how to resolve this

[chetana]

Hi,

Were you able to fix that error? I've just come across the error and never really used FirebrowseR before. Any help would be appreciated! Thanks.

Answer 1

[Haci]

The tutorial subsets only the dead patients: brca.Pats = brca.Pats[ which(brca.Pats$vital_status == "dead"), ]

Otherwise, as the authors state:

downloading mRNA expression data for a thousand patients would take a lot of time, later on.

I suspect that you missed that subsetting step and that is why you are getting the code 414 error. Unfortunately I do not know how to extract all the data, also a newbie.