Question: FirebrowseR retrive all the genes expression
gravatar for rbrtdambrosio
3.9 years ago by
rbrtdambrosio70 wrote:


I'm trying to collect the data from the TCGA COAD project using FirebrowseR. I'm fallowing the "how to use" manual

I would like to modify the following section in order to retrive all the genes expression values for each sample. Unfortunately the function Samples.mRNASeq require a list of gene names. There is a way to retrive all the expression values without specify the single names? Eventually were I could take the full gene list ?

  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 =
                                             page_size = page.Size,
                                             page = page.Counter)
  if(nrow(mRNA.Exp[[page.Counter]]) < page.Size)
    all.Found = T
    page.Counter = page.Counter + 1
mRNA.Exp =, mRNA.Exp)


rna-seq firebrowser • 2.3k views
ADD COMMENTlink modified 3.9 years ago by Mdeng510 • written 3.9 years ago by rbrtdambrosio70

Can we enter all the 20500 genes in genes argument to get all the expression values??

ADD REPLYlink written 3.4 years ago by shashank.jatav30
gravatar for Mdeng
3.9 years ago by
Mdeng510 wrote:

Sadly the API is not designed for these purposes. It's likely more intended to provide a light interface for pre-build queries, which e.g. could be included in an application etc..

To bulk download data sets for an entire cohort I would recommend using GDAC or you could still user FirebrowseR using the Archives.StandardData function. Based on its query parameters it will provide you with a list of archives which can be download, so you don't have to narrow down the bulk data yourself.

ADD COMMENTlink written 3.9 years ago by Mdeng510

oh it's a pity. Thanks for the interesting suggestions!

ADD REPLYlink written 3.9 years ago by rbrtdambrosio70
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