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"

> 

> traceback()

3: stop("unable to find an inherited method for function \"",
fdef@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@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@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@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@rr-research.no

 


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