[BioC] problem with GDS2eSet function in GEOquery package

[James W. MacDonald]

Hi Laurent,

On 2/7/2013 11:52 AM, Laurent Pays [guest] wrote:
> This is the code I used:
> gse<- getGEO(filename='GSE19380_family.soft') with the "GSE19380_family.soft" downloaded on my computer.
>
> Then
>   GDS2eSet(gse, do.log2=FALSE,GPL=NULL,AnnotGPL=TRUE)

I think the problem is that you are getting a GSE object, not a GDS 
object. The easiest thing to do is just get the GSE object and go from 
there:

 > gse <- getGEO("GSE19380")
<snip>
 > gse[[1]]
ExpressionSet (storageMode: lockedEnvironment)
assayData: 31099 features, 26 samples
   element names: exprs
protocolData: none
phenoData
   sampleNames: GSM480943 GSM480944 ... GSM480968 (26 total)
   varLabels: title geo_accession ... data_row_count (33 total)
   varMetadata: labelDescription
featureData
   featureNames: 1367452_at 1367453_at ... AFFX_ratb2/X14115_at (31099
     total)
   fvarLabels: ID GB_ACC ... Gene Ontology Molecular Function (16 total)
   fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
Annotation: GPL1355

So you don't have to convert to an ExpressionSet, as you already have one.

Best,

Jim


>
> And I receive this error:
>
> Error in getGEO(Meta(GDS)$platform, AnnotGPL = AnnotGPL) :
>    You must supply either a filename of a GEO file or a GEO accession
>
> Any help would be appreciated
>
> Thanks in advance
>
>   -- output of sessionInfo():
>
>> sessionInfo()
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>   [1] GEOquery_2.24.1      CellMix_1.1          GSEABase_1.20.1      graph_1.36.1
>   [5] annotate_1.36.0      AnnotationDbi_1.20.3 stringr_0.6.2        Rcpp_0.10.2
>   [9] NMF_0.10.1           Biobase_2.18.0       BiocGenerics_0.4.0   bigmemory_4.3.0
> [13] bigmemory.sri_0.1.2  digest_0.6.2         registry_0.2         rngtools_1.1
> [17] pkgmaker_0.10.1
>
> loaded via a namespace (and not attached):
>   [1] beeswarm_0.1.5        codetools_0.2-8       colorspace_1.2-1
>   [4] corpcor_1.6.4         csSAM_1.2.1           DBI_0.2-5
>   [7] doParallel_1.0.1      foreach_1.4.0         genefilter_1.40.0
> [10] gridBase_0.4-6        gtools_2.7.0          IRanges_1.16.4
> [13] iterators_1.0.6       limSolve_1.5.3        matrixStats_0.6.2
> [16] parallel_2.15.2       preprocessCore_1.20.0 quadprog_1.5-4
> [19] R.methodsS3_1.4.2     RColorBrewer_1.0-5    RCurl_1.95-3
> [22] RSQLite_0.11.2        splines_2.15.2        stats4_2.15.2
> [25] survival_2.37-2       tools_2.15.2          XML_3.95-0.1
> [28] xtable_1.7-0
>
> --
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>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099