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

Laurent Gautier laurent at cbs.dtu.dk
Fri Jun 19 18:13:07 CEST 2009


Lina Cekaite wrote:
> 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.
> 
>  
> 
> 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"


There is no constructor GeneSetCollection() for "GeneSet", 
"EntrezIdentifier", and "KEGGCollection"


I think that it's "GeneSet", "missing", "missing"
or "character", "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"
> 

There is no constructor GeneSetCollection() for "ExpressionSet", 
"AnnDbBimap", and "KEGGCollection"


> 
> 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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