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seandavi / GEOquery

The bridge between the NCBI Gene Expression Omnibus and Bioconductor
http://seandavi.github.io/GEOquery/
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annotating `!Sample` in function 'parseGSEMatrix' #82

Closed woolf-wu closed 5 years ago

woolf-wu commented 5 years ago

Path: GEOquery/R/parseGEO.R Function: parseGSEMatrix GEO: 'GSE113249' or 'GSE113250'

Error:

tmpdat <- read.table( fname, sep="\t", header=FALSE, nrows=samples_header_row_count,
                                   skip=sample_header_start-1)

Solution:

tmpdat <- read.table( fname, sep="\t", header=FALSE, nrows=samples_header_row_count,
                                   skip=sample_header_start-1, fill = T )
seandavi commented 5 years ago

Thanks, @wloof, for the report. I am not seeing any errors with a current version of GEOquery. Could you clarify what error you are getting and what sessionInfo() looks like?

woolf-wu commented 5 years ago

Thanks, @wloof, for the report. I am not seeing any errors with a current version of GEOquery. Could you clarify what error you are getting and what sessionInfo() looks like?

Hi, @seandavi . The real cause is the problem of coding. In my windows, R local setting is 'Chinese'. So I set

Sys.setlocale("LC_ALL","English")

The problem is soveled. The solution I mentioned before is wrong. Thanks for your time.

seandavi commented 5 years ago

Ah, good to know! I'll see if there is a place to get that detail into the documentation.