[BioC] GSEABase on none affy data/mapping problem(?)

[Martin Morgan]

Hi Lina -- 

"Lina Cekaite" <Lina.Cekaite at rr-research.no> writes:

> Dear all, 
>
> I am having problems to run GSEA on none affy data and wonder if someone
> could help. I made an annotation library mapping EntrezIDs using
> AnnotationDbi and I am able to run KEGG using the custom annotated 
>
> package "AB1700sp2.db". But I would like to run trough
> GeneSetCollections()and there I need to map probe IDs to EntrezIDs and
> then do GeneSetCollections().I tried both make an annotated gene set or
> by using ExpressionSet, but end up with the same type of error.

It sounds like you have made a package AB1700sp2.db that successfuly
maps from your probeset identifiers to Entrez identifiers. If so, then

  GeneSetCollection(CRCsubset_map_Q_unique, setType=KEGGCollection())

should work. This requires that annotation(CRCsubset_map_Q_unique)
returns the name of your custom annotation package, i.e.,
"AB1700sp2.db".

Martin

>  
>
> Any ideas what is wrong?
>
>  
>
> Best, Lina
>
>  
>
> ExpressionSet
>
>> CRCsubset_map_Q_unique
>
> ExpressionSet (storageMode: lockedEnvironment)
>
> assayData: 19755 features, 50 samples 
>
>   element names: exprs, se.exprs 
>
> phenoData
>
>   sampleNames: A1_PT, A17_PT, ..., A54_NT  (50 total)
>
>   varLabels and varMetadata description:
>
>     samplename: read from file
>
>     assayname: read from file
>
>     group: read from file
>
> featureData
>
>   featureNames: 160832, 105812, ..., 221132  (19755 total)
>
>   fvarLabels and fvarMetadata description: none
>
> experimentData: use 'experimentData(object)'
>
> Annotation:  
>
>  
>
>> ## Probe annotation to Entrez ids
>
>> probeIds <- featureNames(CRCsubset_map_Q_unique)
>
>> geneIds <- getEG(probeIds, "AB1700sp2")
>
>> gs1<-GeneSet(EntrezIdentifier(), setName="sample.GeneSet2",
> setIdentifier="101",
>
> + geneIds=geneIds)
>
>> ## End(Not run)
>
>> ## Create a new identifier
>
>> setClass("FooIdentifier",
>
> + contains="GeneIdentifierType",
>
> + prototype=prototype(
>
> + type=new("ScalarCharacter", "Foo")))
>
> [1] "FooIdentifier"
>
>> ## Create a constructor (optional)
>
>> FooIdentifier <- function() new("FooIdentifier")
>
>> geneIdType(FooIdentifier())
>
> "Foo"
>
>> ## tidy up
>
>> removeClass("FooIdentifier")
>
> [1] TRUE
>
>> 
>
>> gs1
>
> setName: sample.GeneSet2 
>
> geneIds: 1, 10, ..., 9997 (total: 19755)
>
> geneIdType: EntrezId
>
> collectionType: Null 
>
> details: use 'details(object)'
>
>> 
>
>> 
>
>> gsc<-GeneSetCollection(gs1, idType=EntrezIdentifier(),
> setType=KEGGCollection())
>
> Error in function (classes, fdef, mtable)  : 
>
>   unable to find an inherited method for function "GeneSetCollection",
> for signature "GeneSet", "EntrezIdentifier", "KEGGCollection"
>
>> 
>
>> traceback()
>
> 3: stop("unable to find an inherited method for function \"",
> fdef at generic, 
>
>        "\", for signature ", cnames)
>
> 2: function (classes, fdef, mtable) 
>
>    {
>
>        methods <- .findInheritedMethods(classes, fdef, mtable)
>
>        if (length(methods) == 1L) 
>
>            return(methods[[1L]])
>
>        else if (length(methods) == 0L) {
>
>            cnames <- paste("\"", sapply(classes, as.character), 
>
>                "\"", sep = "", collapse = ", ")
>
>            stop("unable to find an inherited method for function \"", 
>
>                fdef at generic, "\", for signature ", cnames)
>
>        }
>
>        else stop("Internal error in finding inherited methods; didn't
> return a unique method")
>
>    }(list("GeneSet", "EntrezIdentifier", "KEGGCollection"), function
> (object, 
>
>        ..., idType, setType) 
>
>    standardGeneric("GeneSetCollection"), <environment>)
>
> 1: GeneSetCollection(gs1, idType = EntrezIdentifier(), setType =
> KEGGCollection())
>
>  
>
>> 
>
>> map <- getAnnMap("ENTREZID", "AB1700sp2.db", load=TRUE, type=c("db"))
>
>> gsc<-GeneSetCollection(CRCsubset_map_Q_unique,
> idType=map,setType=KEGGCollection())
>
> Error in function (classes, fdef, mtable)  : 
>
>   unable to find an inherited method for function "GeneSetCollection",
> for signature "ExpressionSet", "AnnDbBimap", "KEGGCollection"
>
>> 
>
>> traceback()
>
> 3: stop("unable to find an inherited method for function \"",
> fdef at generic, 
>
>        "\", for signature ", cnames)
>
> 2: function (classes, fdef, mtable) 
>
>    {
>
>        methods <- .findInheritedMethods(classes, fdef, mtable)
>
>        if (length(methods) == 1L) 
>
>            return(methods[[1L]])
>
>        else if (length(methods) == 0L) {
>
>            cnames <- paste("\"", sapply(classes, as.character), 
>
>                "\"", sep = "", collapse = ", ")
>
>            stop("unable to find an inherited method for function \"", 
>
>                fdef at generic, "\", for signature ", cnames)
>
>        }
>
>        else stop("Internal error in finding inherited methods; didn't
> return a unique method")
>
>    }(list("ExpressionSet", "AnnDbBimap", "KEGGCollection"), function
> (object, 
>
>        ..., idType, setType) 
>
>    standardGeneric("GeneSetCollection"), <environment>)
>
> 1: GeneSetCollection(CRCsubset_map_Q_unique, idType = map, setType =
> KEGGCollection())
>
>> 
>
>> sessionInfo()
>
> R version 2.9.0 (2009-04-17) 
>
> i386-pc-mingw32 
>
>  
>
> locale:
>
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
>  
>
> attached base packages:
>
> [1] tools     stats     graphics  grDevices utils     datasets  methods
> base     
>
>  
>
> other attached packages:
>
>  [1] GO.db_2.2.11        KEGG.db_2.2.11      Ruuid_1.22.0
> GSEABase_1.6.0      RBGL_1.20.0        
>
>  [6] graph_1.22.2        genefilter_1.24.0   Category_2.10.0
> annotate_1.22.0     RColorBrewer_1.0-2 
>
> [11] AB1700sp2.db_1.0.0  RSQLite_0.7-1       DBI_0.2-4
> AnnotationDbi_1.6.0 Biobase_2.4.1      
>
>  
>
> loaded via a namespace (and not attached):
>
> [1] splines_2.9.0   survival_2.35-4 XML_2.5-1       xtable_1.5-5   
>
>  
>
> Lina Cekaite, PhD
>
> Department of Cancer Prevention
>
> Rikshospitalet University Hospital
>
> Faculty Division, The Norwegian Radium Hospital, 
>
> University of Oslo, 0316 Oslo
>
> NORWAY
>
>  
>
> Email: linac at rr-research.no
>
>  
>
>
> 	[[alternative HTML version deleted]]
>
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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 M1 B861
Phone: (206) 667-2793