[BioC] GEOquery and GSE error

[Ovokeraye Achinike-Oduaran]

Hi Sean,

Thanks. I'm thinking I have the latest version because I only very
recently installed the package.

[1] GEOquery_2.19.3 Biobase_2.12.2 .

Is there a more recent one?

Thanks.

Avoks

On Tue, Sep 20, 2011 at 3:37 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> Hi, Avoks.
>
> Without sessionInfo(), it is not possible to be sure what version of
> GEOquery you are running, but I would suggest you upgrade to the
> newest version of GEOquery.  I think that will fix the issue.
>
> Sorry for the inconvenience.
>
> Sean
>
>
> On Tue, Sep 20, 2011 at 9:24 AM, Ovokeraye Achinike-Oduaran
> <ovokeraye at gmail.com> wrote:
>> Hi all,
>>
>> I am unable to access a series file even though I get a message that
>> it saved to a local directory, albeit with an error message and a
>> number of warnings, after retrieval with GEOquery. Any ideas as to
>> what I may be doing wrong?
>>
>> Thanks.
>>
>> Avoks
>>
>>> gse9006 = getGEO("GSE9006", GSEMatrix = TRUE)
>> Found 2 file(s)
>> GSE9006-GPL96_series_matrix.txt.gz
>> trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE9006/GSE9006-GPL96_series_matrix.txt.gz'
>> ftp data connection made, file length 5775933 bytes
>> opened URL
>> downloaded 5.5 Mb
>>
>> File stored at:
>> C:\...\Temp\RtmpJM0ZOp/GPL96.soft
>> Error in validObject(.Object) :
>>  invalid class "ExpressionSet" object: featureNames differ between
>> assayData and featureData
>> In addition: Warning messages:
>> 1: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) :
>>  seek on a gzfile connection returned an internal error
>> 2: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) :
>>  seek on a gzfile connection returned an internal error
>> 3: In readLines(con, 1) :
>>  seek on a gzfile connection returned an internal error
>> 4: In read.table(file = file, header = header, sep = sep, quote = quote,  :
>>  seek on a gzfile connection returned an internal error
>> 5: In read.table(file = file, header = header, sep = sep, quote = quote,  :
>>  seek on a gzfile connection returned an internal error
>> 6: In read.table(file = file, header = header, sep = sep, quote = quote,  :
>>  seek on a gzfile connection returned an internal error
>> 7: In read.table(file = file, header = header, sep = sep, quote = quote,  :
>>  not all columns named in 'colClasses' exist
>>
>>> gse9006
>> Error: object 'gse9006' not found
>>
>>> show(gse9006)
>> Error in show(gse9006) :
>>  error in evaluating the argument 'object' in selecting a method for
>> function 'show': Error: object 'gse9006' not found
>>
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>