Question: GEOquery getGEO() Error in open.connection(x, "rb") : HTTP error 403.
3
gravatar for dmbergau
17 months ago by
dmbergau30
dmbergau30 wrote:

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?

geoquery R getgeo • 2.1k views
ADD COMMENTlink modified 17 months ago by meunier0 • written 17 months ago by dmbergau30
1

Same problem here.

ADD REPLYlink modified 17 months ago • written 17 months ago by Kevin Blighe65k

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

ADD REPLYlink modified 17 months ago • written 17 months ago by Kevin Blighe65k
1

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.

ADD REPLYlink modified 17 months ago • written 17 months ago by Sean Davis26k

Yep, cheers Sean.

ADD REPLYlink written 17 months ago by Kevin Blighe65k
1

I would suggest reporting issues to NCBI GEO staff (geo@ncbi.nlm.nih.gov). I agree that recent behavior of GEO has been more spotty than previous.

ADD REPLYlink modified 17 months ago • written 17 months ago by Sean Davis26k

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.

ADD REPLYlink modified 17 months ago • written 17 months ago by Shicheng Guo8.3k

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.

ADD REPLYlink written 17 months ago by meunier0

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.

ADD REPLYlink modified 17 months ago • written 17 months ago by meunier0
1
gravatar for Sean Davis
17 months ago by
Sean Davis26k
National Institutes of Health, Bethesda, MD
Sean Davis26k wrote:

It looks like the problem has been resolved.

ADD COMMENTlink written 17 months ago by Sean Davis26k

Thanks Seán

ADD REPLYlink written 17 months ago by Kevin Blighe65k
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