I've been successfully using GEOquery to download GEO datasets. I came across one (GSE56046) whose SOFT file seemed too small for the number of samples, and I get a lot of downstream errors (see below).
Before contacting the submitter, can anyone spot what the issue is?
This command downloads 1203 sample data surprisingly fast and results in a 61 Mb dataset, which is surprisingly small.
gse = getGEO("GSE56046",GSEMatrix=F)
This also results in warning messages:
Warning messages: 1: In readLines(con, n = chunksize) : seek on a gzfile connection returned an internal error
There is also something fishy about the S4 object:
Error in gse[] : this S4 class is not subsettable