Question: Unable to download the RNA-seq counts file using RnaSeqGeneEdgeRQL and HTTP status was '404 Not Found
0
gravatar for mohammedtoufiq91
10 months ago by
mohammedtoufiq91110 wrote:

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

ADD COMMENTlink modified 10 months ago by Mark800 • written 10 months ago by mohammedtoufiq91110
2
gravatar for Mark
10 months ago by
Mark800
Mark800 wrote:

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.

ADD COMMENTlink written 10 months ago by Mark800
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