[BioC] GSEABase

[Martin Morgan]

Hi John --

"John Lande" <john.lande77 at gmail.com> writes:

> Dear Bioc,
>
> I am using the package GSEABase, and I have the following error.
> I imput eset in the function GeneSetCollection, but I do retrive the
> following error. I am using Illumna datata,
> and transformed the lumi.batch in expression set.
>
>> gsc <- GeneSetCollection(eset,
> +    setType = KEGGCollection()
> + )
> Error in validObject(.Object) :
>   invalid class "ScalarCharacter" object: ScalarCharacter must have length
> one

It's a little hard to know exactly what is going wrong for you;
the output of traceback() might help. Also, GeneSetCollection creates
a list of GeneSet's. R has this to say about the GeneSet class:

> getClass("GeneSet")
Class "GeneSet"

Slots:
                                                               
Name:          geneIdType            geneIds            setName
Class: GeneIdentifierType          character    ScalarCharacter
                                                               
Name:       setIdentifier   shortDescription    longDescription
Class:    ScalarCharacter    ScalarCharacter    ScalarCharacter
                                                               
Name:            organism          pubMedIds               urls
Class:    ScalarCharacter          character          character
                                                               
Name:         contributor            version       creationDate
Class:          character           Versions          character
                         
Name:      collectionType
Class:     CollectionType

Known Subclasses: "GeneColorSet"

The error you see comes from one of setName, setIdentifier,
shortDescription, longDescription, or organism being created with
a character vector that is either empty or has more than 1 entry.

My best guess is shortDescription, which comes from
experimentData(eset)@title, or longDescription, from abstract(eset).

Other possibilities:

setName comes from the keys of the "PATH2PROBE"  map in the organism
you're using. Should be OK.

setIdentifier should be auto-generated with
GSEABase:::.uniqueIdentifier(). Should be OK.

'organism' comes from the 'annotation' slot of the ExpressionSet

  getAnnMap("ORGANISM", annotation(eset))

or is set to "" if there is no annotation information. Should be OK.

Does that help?

Martin

> thank you
>
>> sessionInfo()
> R version 2.8.0 (2008-10-20)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
>  [1] genefilter_1.22.0        GSEABase_1.4.0
> graph_1.20.0
>  [4] ROC_1.16.0               maxstat_0.7-12
> mvtnorm_0.9-2
>  [7] exactRankTests_0.8-17    survival_2.34-1
> biomaRt_1.16.0
> [10] limma_2.16.3             annaffy_1.14.0
> KEGG.db_2.2.5
> [13] GO.db_2.2.5              illuminaHumanv2.db_1.1.3
> Mfuzz_1.12.0
> [16] e1071_1.5-18             class_7.2-44
> Heatplus_1.12.0
> [19] lumi_1.8.3               RSQLite_0.7-1
> DBI_0.2-4
> [22] preprocessCore_1.4.0     mgcv_1.4-1
> affy_1.20.0
> [25] annotate_1.20.1          xtable_1.5-4
> AnnotationDbi_1.4.1
> [28] Biobase_2.2.1
>
> loaded via a namespace (and not attached):
> [1] affyio_1.10.1   cluster_1.11.11 RCurl_0.92-0    XML_1.98-1
>
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>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793