[BioC] GEOquery::parseGEO throws error reading file

Sean Davis sdavis2 at mail.nih.gov
Fri Aug 1 17:36:15 CEST 2008

On Sun, Jul 27, 2008 at 11:44 PM, Gad Abraham
<gabraham at csse.unimelb.edu.au> wrote:
> Hi,
> I'm using GEOquery 2.4.1 to read an NCBI GEO file
> ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE4284/GSE4284_series_matrix.txt.gz
>  but parseGEO throws an error. The switch argument evaluates to "0", which
> doesn't match alternative, so it tries to match on the last empty argument
> and fails. I don't know if this is related to the warnings; the file
> contains text such as manufacturer\xa1\xafs which may not parse correctly.
> Below is the output.
> Thanks for any advice,
> Gad
>> g <- getGEO(filename="GSE4284_series_matrix.txt")

Hi, Gad.  The filename argument does not yet take GSE series matrix
files as an argument.  I have a couple of changes to make with GSE
series matrix handling and adding file-based parsing is one of them.


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