[BioC] GEOquery and GSE error

[Sean Davis]

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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