Question: Unable to download the RNA-seq counts file using RnaSeqGeneEdgeRQL and HTTP status was '404 Not Found
0
gravatar for mohammedtoufiq91
5 weeks ago by
mohammedtoufiq9190 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 5 weeks ago by Amar620 • written 5 weeks ago by mohammedtoufiq9190
2
gravatar for Amar
5 weeks ago by
Amar620
Amar620 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 5 weeks ago by Amar620
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1115 users visited in the last hour