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Lina Cekaite
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40
@lina-cekaite-3516
Last seen 10.3 years ago
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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