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:  LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252  LC_MONETARY=English_United States.1252 LC_NUMERIC=C  LC_TIME=English_United States.1252 attached base packages:  parallel stats graphics grDevices utils datasets methods base other attached packages:  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?