Thank you, Robert.

The previous suggestion worked, so it was related to annotation despite the
fact that I manually installed it.
I will use yours further on GSVA analyses!


On Wed, Apr 17, 2013 at 12:24 PM, Robert Castelo <robert.castelo@upf.edu>wrote:

> Dear Zhenya,
>
> from your output below i'd say that the problem arises when mapping
> identifiers between the genes in gene sets from the 'GeneSetCollection'
> object and the features from the 'ExpressionSet' object.
>
> my guess is that the problematic instruction would be this line, i'm
> putting it here trying to use your variable names, please run it and paste
> here the result:
>
> library(Biobase)
> library(GSEABase)
>
> mapped.gset.idx.list <- mapIdentifiers(gsc, AnnoOrEntrezIdentifier(**
> annotation(EsetData_f)))
>
> if this lines prompts an error, then in principle this is not as much of a
> problem of GSVA but of how the identifier mapping magic should be working,
> and maybe the maintainers of GSEABase can give you a hand there.
>
> please also paste the output of traceback() right after you get the error
> and also the display of the objects 'gsc' and 'EsetData_f'
>
>
> cheers,
> robert.
>
>
> On 04/17/2013 06:02 PM, Zhenya [guest] wrote:
>
>>
>> Hi All,
>>
>> I am trying to run the code for GSVA (library with the same name). The
>> code is below, but the main error is around annotation:
>>
>>> source("http://bioconductor.**org/biocLite.R<http://bioconductor.org/biocLite.R>
>>> ")
>>>
>> Bioconductor version 2.12 (BiocInstaller 1.10.0), ?biocLite for help
>>
>>> biocLite("hthgu133pluspm.db")
>>>
>> BioC_mirror: http://bioconductor.org
>> Using Bioconductor version 2.12 (BiocInstaller 1.10.0), R version 3.0.0.
>> Installing package(s) 'hthgu133pluspm.db'
>> Warning message:
>> package ‘hthgu133pluspm.db’ is not available (for R version 3.0.0)
>>
>>
>> Code:
>>
>> # CREATE GeneSetCollection
>> library(GSEABase)
>> x<- scan("GeneSets.gmt", what="", sep="\n")
>> GeneSets.gmt<- strsplit(x, "[[:space:]]+")
>> names(GeneSets.gmt)<- sapply(GeneSets.gmt, `[[`, 1)
>> GeneSets.gmt<- lapply(GeneSets.gmt, `[`, -1)
>> n<- names(GeneSets.gmt)
>> uniqueList<- lapply(GeneSets.gmt, unique)
>> makeSet<- function(geneIds, n) {GeneSet(geneIds,
>> geneIdType=SymbolIdentifier(), setName=n)}
>> gsList<- gsc<- mapply(makeSet, uniqueList[], n)
>> gsc<- GeneSetCollection(gsList)
>>
>> # DATASET
>> # CREATE ExpressionSet
>> exprs<- as.matrix(read.table("**ExprData.txt", header=TRUE, sep="\t",
>> row.names=1, as.is=TRUE))
>> pData<- read.table("DesignFile.txt",**row.names=1, header=T,sep="\t")
>> phenoData<- new("AnnotatedDataFrame",data=**pData)
>> annotation<- "hthgu133pluspm.db"
>> EsetData<- ExpressionSet(assayData=exprs,**phenoData=phenoData,**
>> annotation="hthgu133pluspm")
>> head(ExprData)
>>
>> #Gene Filtering
>> library(genefilter)
>> library("hthgu133pluspm")
>> filtered_eset<- nsFilter(EsetData, require.entrez=TRUE,
>> remove.dupEntrez=TRUE, var.func=IQR, var.filter=FALSE, var.cutoff=0.25,
>> filterByQuantile=TRUE, feature.exclude="^AFFX")
>> # get stats for numbers of probesets removed
>> filtered_eset
>> EsetData_f<- filtered_eset$eset
>>
>> # GSVA
>> library(GSVA)
>> gsva_es<- gsva(EsetData_f,gsc,abs.**ranking=FALSE,min.sz=1,max.sz=**
>> 1000,mx.diff=TRUE)$es.obs
>>
>> I downloaded hthgu133pluspm from http://nmg-r.bioinformatics.**
>> nl/NuGO_R.html <http://nmg-r.bioinformatics.nl/NuGO_R.html>
>> and R still complains. The available on Bioconductor:
>> hthgu133pluspmprobe
>> and
>> hthgu133pluspmcdf
>> are not correct and give error for nsFilter and gsva:
>> Error in (function (classes, fdef, mtable)  :
>>    unable to find an inherited method for function ‘cols’ for
>> signature ‘"environment"’
>>
>> Mapping identifiers between gene sets and feature names
>> Error in GeneSetCollection(lapply(what, mapIdentifiers, to, ..., verbose
>> = verbose)) :
>>    error in evaluating the argument 'object' in selecting a method for
>> function 'GeneSetCollection': Error in (function (classes, fdef, mtable)  :
>>    unable to find an inherited method for function ‘cols’ for
>> signature ‘"environment"’
>>
>>
>> Thank you,
>> Zhenya
>>
>>   -- output of sessionInfo():
>>
>> R version 3.0.0 (2013-04-03)
>> Platform: i386-w64-mingw32/i386 (32-bit)
>>
>> locale:
>> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
>> States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C
>> [5] LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] parallel  stats     graphics  grDevices utils     datasets  methods
>> base
>>
>> other attached packages:
>>   [1] GSVA_1.8.0                 BiocInstaller_1.10.0
>> hthgu133pluspmprobe_2.12.0 hthgu133pluspmcdf_2.12.0   genefilter_1.42.0
>>      GSEABase_1.22.0
>>   [7] graph_1.38.0               annotate_1.38.0
>>  AnnotationDbi_1.22.1       Biobase_2.20.0             BiocGenerics_0.6.0
>>
>> loaded via a namespace (and not attached):
>> [1] DBI_0.2-5       IRanges_1.18.0  RSQLite_0.11.2  splines_3.0.0
>> stats4_3.0.0    survival_2.37-4 tools_3.0.0     XML_3.96-1.1    xtable_1.7-1
>>
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
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>>
>>
> --
> Robert Castelo, PhD
> Associate Professor
> Dept. of Experimental and Health Sciences
> Universitat Pompeu Fabra (UPF)
> Barcelona Biomedical Research Park (PRBB)
> Dr Aiguader 88
> E-08003 Barcelona, Spain
> telf: +34.933.160.514
> fax: +34.933.160.550
>

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