[BioC] GEOquery and GSE error

[Sean Davis]

On Tue, Sep 20, 2011 at 9:44 AM, Ovokeraye Achinike-Oduaran
<ovokeraye at gmail.com> wrote:
> 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?

Yes.  2.19.4 is the most recent version.

Sean


> 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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>>
>
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