Question: mRNA.Exp[[page.Counter]] : subscript out of bounds
0
gravatar for j11patel
23 months ago by
j11patel0
j11patel0 wrote:

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

firebrowse samples.mrnaseq R • 738 views
ADD COMMENTlink modified 22 months ago by Haci20 • written 23 months ago by j11patel0

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.

ADD REPLYlink written 25 days ago by chetana40
0
gravatar for Haci
22 months ago by
Haci20
Haci20 wrote:

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.

ADD COMMENTlink written 22 months ago by Haci20
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