[BioC] GSEA

[James W. MacDonald]

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
> 
>  
> 
>  
> 
> 
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> 
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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