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$tcga_participant_barcode,
page_size = page.Size,
page = page.Counter)
if(nrow(mRNA.Exp[[page.Counter]]) < page.Size)
all.Found = T
else
page.Counter = page.Counter + 1
} mRNA.Exp = do.call(rbind, mRNA.Exp)
dim(mRNA.Exp)
Please let me know how to resolve this
•
written
by
j11patel •
1 answer
The tutorial subsets only the dead patients: brca.Pats = brca.Pats[ which(brca.Pats$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.
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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.