I cant seem to use
GEOquery::getGEO(). I get
Error in open.connection(x, "rb") : HTTP error 403 . everything worked before the weekend but it seems now it doesn't
> getGEO("GSE5364") Error in open.connection(x, "rb") : HTTP error 403.
This happens for every accession number.
When i garbage collect with
gc() i get:
> Warning messages: 1: In .Internal(gc(verbose, reset, full)) : > closing unused connection 6 > (https://ftp.ncbi.nlm.nih.gov/geo/series/GSE5nnn/GSE5364/matrix/)
When trying to access this URL, it doesn't seem to exist anymore. The parent directory does however: https://ftp.ncbi.nlm.nih.gov/. Albeit it doesnt seem to have a subfolder for GEO anymore?
Alternatively, ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE5nnn/GSE5364/ does exist.
Question 1: Is anyone else having this issue and has something happened to the GEO directory within NCBI?
Question 2: Can i change the URL that GEOquery uses to pull the data to ftp://ftp.ncbi.nlm.nih.gov.
I know i can download them and access them locally but i will be using a lot of series and so wanted to use getGEO's ability to pull this information with just accession numbers.
Thanks in advance!
> sessionInfo() R version 3.5.3 (2019-03-11) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 8.1 x64 (build 9600) Matrix products: default locale:  LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252  LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C  LC_TIME=English_United Kingdom.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