[BioC] nsFilter error in genefilter

[Zhenya [guest]]

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")
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
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   


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