[BioC] GEOquery not parsing GSE expression sets

[Sean Davis]

On Thu, Apr 4, 2013 at 12:09 PM, Lucas Santana dos Santos
<santanasantosl at me.com> wrote:
> Hi Sean,
>
> I think I might know the source of error. GEOquery works fine before I load the 'mvbutils' package.
> Once I load it I starting getting the error...

I'll look into it.  Thanks for the hint.

Sean


> Thanks,
>
> Lucas
>
> On Apr 4, 2013, at 12:00 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>
>> On Thu, Apr 4, 2013 at 11:51 AM, Lucas Santana dos Santos
>> <santanasantosl at me.com> wrote:
>>> All,
>>>
>>> I have been trying to use the function getGEO, part of GEOquery package to retrieve GSE objects.
>>> However, I am getting the following error message:
>>>
>>> data/GEO> gse2553 <- getGEO('GSE2553',GSEMatrix=TRUE)
>>> Found 1 file(s)
>>> GSE2553_series_matrix.txt.gz
>>> Using locally cached version: /var/folders/z4/hzbhqd1j3gzc4mqhq29fqb240000gr/T//Rtmpb3s3hN/GSE2553_series_matrix.txt.gz
>>> Error in `row.names<-.data.frame`(`*tmp*`, value = value) :
>>> invalid 'row.names' length
>>>
>>> I get the same error no matter which GEO GSE id I use. It seems to be a parsing error, when creating a data frame
>>> This was suppose to work, as this code snippet is from the "Using the GEOquery package" PDF (page 13: http://www.bioconductor.org/packages/2.11/bioc/vignettes/GEOquery/inst/doc/GEOquery.pdf).
>>>
>>> Any thoughts about what id the cause of error or how to fix it?
>>
>> Hi, Lucas.
>>
>> Could you send the output of sessionInfo()?  Also, could you try this
>> in a new R session?  It appears that GEOquery is picking up a cached
>> version of the series matrix file that might be corrupted.
>>
>> Sean
>>
>>>
>>> Thank you very much,
>>>
>>>
>>> Lucas
>>>        [[alternative HTML version deleted]]
>>>
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