[BioC] GSEA
James W. MacDonald
jmacdon at med.umich.edu
Fri Oct 16 19:10:27 CEST 2009
Hi Nikolaus,
Nikolaus Schantz wrote:
> Dear Bioconductors,
>
>
>
> I tried to apply the code in "An Introduction to GSEABase" to my
> ExpressionSet.
>
>
>
> Everything works fine until I got the following error message:
>
>
>
>> mapIdentifiers(egs, EntrezIdentifier())
>
> Fehler: getAnnMap: package ra1r3cdf_1.22.0 not available
>
>
>
> Here is some more information:
>
>
>
>> eset
>
> ExpressionSet (storageMode: lockedEnvironment)
>
> assayData: 29214 features, 26 samples
>
> element names: exprs
>
> phenoData
>
> sampleNames: A1_3, A1_4, ..., T3_3 (26 total)
>
> varLabels and varMetadata description:
>
> Substance: Substance
>
> Period: Incubation Period
>
> PrPe: Probe.Period
>
> featureData
>
> featureNames: 10700001, 10700002, ..., 10940690 (29214 total)
>
> fvarLabels and fvarMetadata description: none
>
> experimentData: use 'experimentData(object)'
>
> Annotation: ra1r3cdf_1.22.0
This is undoubtedly the source of your problem. The annotation of your
ExpressionSet shouldn't be something like that. The most likely correct
annotation is 'ra1r3', assuming this is a custom chip of that name.
However, looking at your sessionInfo(), I get the impression that this
might actually be a rat gene st chip, and if I further surmise that you
want to annotate using the ragene10sttranscriptcluster.db_1.0.1 package
you have attached, then the annotation should be
'ragene10sttranscriptcluster'.
If I have guessed correctly, then you should be able to proceed after
adjusting the annotation slot of your ExpressionSet:
annotation(eset) <- "ragene10sttranscriptcluster"
Best,
Jim
>
>
>
>> sessionInfo()
>
> R version 2.9.0 (2009-04-17)
>
> i386-pc-mingw32
>
>
>
> locale:
>
> LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=
> German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252
>
>
>
> attached base packages:
>
> [1] stats graphics grDevices utils datasets methods base
>
>
>
>
> other attached packages:
>
> [1] ra1r3cdf_1.22.0 GO.db_2.2.11
>
>
> [3] ragene10sttranscriptcluster.db_1.0.1 RSQLite_0.7-1
>
>
> [5] DBI_0.2-4 GSEABase_1.6.1
>
>
> [7] graph_1.22.2 annotate_1.22.0
>
>
> [9] AnnotationDbi_1.6.1 Biobase_2.4.1
>
>
>
>
> loaded via a namespace (and not attached):
>
> [1] tools_2.9.0 XML_2.5-1 xtable_1.5-5
>
>
>
> Any help is appreciated
>
> Thank you
>
> Nikolaus
>
>
>
>
>
>
> [[alternative HTML version deleted]]
>
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--
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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