[BioC] getGEO error?

[James F. Reid]

Hi Hendrick,


On 29/02/12 06:46, Hendrik Falk wrote:
> Hi list,
>
> I'm trying to analyse GeneExpressionOmnibus data using the Biobase package. For the
> GSE record GSE4922 I get an error as shown below, whereas other records (e.g.
> GSE1456) load without problems. Is there an easy way to fix the problem or get
> around it?
>
> Best Regards,
> Hendrik
>
>> GSE4922<- getGEO("GSE4922",GSEMatrix=TRUE)
> Found 4 file(s)
> GSE4922-GPL96_series_matrix-1.txt.gz
> trying URL
> 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE4922/GSE4922-GPL96_series_matrix-1.txt.gz'
> ftp data connection made, file length 44890082 bytes
> opened URL
> downloaded 42.8 Mb
>
> Using locally cached version of GPL96 found here:
> C:\DOCUME~1\falk\LOCALS~1\Temp\RtmpAjqjX7/GPL96.soft
> Error in validObject(.Object) :
>    invalid class “ExpressionSet” object: featureNames differ between assayData and
> featureData
>>

it works on my side (see sessionInfo() below), make sure your packages 
are up-to-date and that the download was not interrupted.

HTH
J.

> sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
  [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
  [7] LC_PAPER=C                 LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  tools     methods
[8] base

other attached packages:
[1] GEOquery_2.20.8 Biobase_2.14.0

loaded via a namespace (and not attached):
[1] RCurl_1.91-1 XML_3.9-4