GEOquery getGEO() Error in open.connection(x, "rb") : HTTP error 403.

Question

[dmbergau]

I am trying to download a number of GSE datasets with GEOquery using codes that looks like the following

library(GEOquery)
library(Biobase)
library(limma)

gset <- getGEO("GSE54884", GSEMatrix =TRUE, getGPL=FALSE)

and I am receiving this error:

Error in open.connection(x, "rb") : HTTP error 403.

Here is my session information:

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows >= 8 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] GEOquery_2.50.5     Biobase_2.42.0      BiocGenerics_0.28.0

This seems to work for other GSE datasets such as:

gse <- getGEO("GSE781",GSEMatrix=FALSE)

My understanding is that HTTP error 403 is an access issue, but I thought all GEO Datasets are open access. Any ideas about what I might be doing wrong?

[Kevin Blighe]

Same problem here.

[Kevin Blighe]

Related post is on Bioconductor: https://support.bioconductor.org/p/120475/

[Sean Davis]

Just to be clear, the reported problem here is due to a problem at NCBI, not with GEOquery. Until NCBI resolves its network/hosting issues, access via GEOquery will not work.

[Kevin Blighe]

Yep, cheers Sean.

[Sean Davis]

I would suggest reporting issues to NCBI GEO staff ([e-mail]). I agree that recent behavior of GEO has been more spotty than previous.

[Shicheng Guo]

It looks such situation frequently occurred recently. Before that, I seldom meet such problem. Maybe it will be helpful to send a email to GEO database service stuff. One of the solution is that you try for multiple times and sometimes it works.

[meunier]

For a workaround with microarray series, manually download the "GSExxxx_series_matrix.txt.gz" file from the GEO Accession page ("Series Matrix File(s)" link in "Download Family" section) and specify the filename in the getGEO function call to its location.

[meunier]

It seems that the GEO ftp pages to download the series matrix files are unavailable and the GEOquery error has changed to a 404.

Edit: Resolved.

Answer 1

[Sean Davis]

It looks like the problem has been resolved.

[Kevin Blighe]

Thanks Seán