Unable to download the RNA-seq counts file using RnaSeqGeneEdgeRQL and HTTP status was '404 Not Found
1
0
Entering edit mode
5.0 years ago

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

RNA-Seq RnaSeqGeneEdgeRQL • 985 views
ADD COMMENT
2
Entering edit mode
5.0 years ago
Mark ★ 1.6k

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 COMMENT

Login before adding your answer.

Traffic: 1031 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6