Unable to download the RNA-seq counts file using RnaSeqGeneEdgeRQL and HTTP status was '404 Not Found

Question

[mohammedtoufiq91]

Hi,

I am using the RnaSeqGeneEdgeRQL library to perform some analysis using the RNA-Seq count data (GSE113964_RNASeqMatBloodCount_Tarca.csv.gz) present in the GSE113964 using the below code. I am getting the error message. Is this a network related issue?

library(RnaSeqGeneEdgeRQL)
FileURL <- paste(
  "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi",
  "format=file",
  "file=GSE113964_RNASeqMatBloodCount_Tarca.csv.gz",
  sep="&")
download.file(FileURL, "GSE113964_RNASeqMatBloodCount_Tarca.csv.gz")

download.file(FileURL, "GSE113964_RNASeqMatBloodCount_Tarca.csv.gz")

trying URL 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi&format=file&file=GSE113964_RNASeqMatBloodCount_Tarca.csv.gz'
Error in download.file(FileURL, "GSE113964_RNASeqMatBloodCount_Tarca.csv.gz") : 
  cannot open URL 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi&format=file&file=GSE113964_RNASeqMatBloodCount_Tarca.csv.gz'
In addition: Warning message:
In download.file(FileURL, "GSE113964_RNASeqMatBloodCount_Tarca.csv.gz") :
  cannot open URL 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi&format=file&file=GSE113964_RNASeqMatBloodCount_Tarca.csv.gz': HTTP status was '404 Not Found'

Thank you,
Toufiq

Answer 1

[Mark]

It looks like NCBI might have changed how links are generated.

https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE113964&format=file&file=GSE113964%5FRNASeqMatBloodCount%5FTarca%2Ecsv%2Egz

vs

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi&format=file&file=GSE113964_RNASeqMatBloodCount_Tarca.csv.gz

For learning how to perform DE analysis (which is the purpose of that package), I would manually download the files required and move onto the real DE analysis. If you want to automate the download process, there's better methods.