Dear Jim,

I am facing the same problem, and your idea would be great for me but I ran
into a problem: cannot change featureNames of Affybatch.

> my.data
my.data
AffyBatch object
size of arrays=744x744 features (23 kb)
cdf=HT_HG-U133_Plus_PM (54715 affyids)
number of samples=16
number of genes=54715
annotation=hthgu133pluspm
notes=

> featureNames(my.data) <- gsub("_PM","", featureNames(my.data))

Error in `featureNames<-`(`*tmp*`, value = c("1007_s_at", "1053_at",
"117_at",  :
 * Cannot change featureNames of AffyBatch*

I tried running R as super user but same result.
I also want to replace the default cdf by a brainarray cdf after this step.

ps. I can perform vsnrma(), but e.g. nsFilter apparently needs the
annotation file so I have to switch to the plus2 or make the
"hthgu133pluspm.db" package (which I never tried before)
Do you have any suggestions on the *Cannot change featureNames of AffyBatch?
*


R version 3.0.1 (2013-05-16)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
base

other attached packages:
 [1] hthgu133pluspmcdf_2.12.0          genefilter_1.42.0
vsn_3.28.0
 [4] arrayQualityMetrics_3.16.0        hgu133plus2.db_2.9.0
org.Hs.eg.db_2.9.0
 [7] RSQLite_0.11.4                    DBI_0.2-7
hthgu133pluspmhsentrezgcdf_17.1.0
[10] AnnotationDbi_1.22.5              limma_3.16.5
affy_1.38.1
[13] Biobase_2.20.0                    BiocGenerics_0.6.0

loaded via a namespace (and not attached):
 [1] affyio_1.28.0         affyPLM_1.36.0        annotate_1.38.0
beadarray_2.10.0      BeadDataPackR_1.12.0  BiocInstaller_1.10.2
 [7] Biostrings_2.28.0     Cairo_1.5-2           cluster_1.14.4
colorspace_1.2-2      gcrma_2.32.0          grid_3.0.1
[13] Hmisc_3.10-1.1        hwriter_1.3           IRanges_1.18.1
lattice_0.20-15       latticeExtra_0.6-24   plyr_1.8
[19] preprocessCore_1.22.0 RColorBrewer_1.0-5    reshape2_1.2.2
setRNG_2011.11-2      splines_3.0.1         stats4_3.0.1
[25] stringr_0.6.2         survival_2.37-4       SVGAnnotation_0.93-1
tools_3.0.1           XML_3.98-1.1          xtable_1.7-1
[31] zlibbioc_1.6.0


2013/4/17 James W. MacDonald <jmacdon@uw.edu>

> Hi Zhenya,
>
>
> On 4/17/2013 12:02 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")
>>>
>>
> There is no such package. You could easily create one yourself using the
> AnnotationForge package (see the vignette). Or you could note that the
> hthgu133pluspm array has identical content as the hgu133plus2 array, except
> for a few extra control probesets, and the fact that they insisted on
> adding an extra _PM to all the probesets.
>
> > sum(ls(hgu133plus2cdf) %in% gsub("_PM","", ls(hthgu133pluspmcdf)))
> [1] 54675
> > length(ls(hgu133plus2cdf))
> [1] 54675
> > length(ls(hthgu133pluspmcdf))
> [1] 54715
> > ls(hthgu133pluspmcdf)[!gsub("_**PM","", ls(hthgu133pluspmcdf)) %in%
> ls(hgu133plus2cdf)]
> [1] "AFFX-NonspecificGC10_at" "AFFX-NonspecificGC11_at"
> [3] "AFFX-NonspecificGC12_at" "AFFX-NonspecificGC13_at"
> [5] "AFFX-NonspecificGC14_at" "AFFX-NonspecificGC15_at"
> [7] "AFFX-NonspecificGC16_at" "AFFX-NonspecificGC17_at"
> [9] "AFFX-NonspecificGC18_at" "AFFX-NonspecificGC19_at"
> [11] "AFFX-NonspecificGC20_at" "AFFX-NonspecificGC21_at"
> [13] "AFFX-NonspecificGC22_at" "AFFX-NonspecificGC23_at"
> [15] "AFFX-NonspecificGC24_at" "AFFX-NonspecificGC25_at"
> [17] "AFFX-NonspecificGC3_at" "AFFX-NonspecificGC4_at"
> [19] "AFFX-NonspecificGC5_at" "AFFX-NonspecificGC6_at"
> [21] "AFFX-NonspecificGC7_at" "AFFX-NonspecificGC8_at"
> [23] "AFFX-NonspecificGC9_at" "AFFX-r2-TagA_at"
> [25] "AFFX-r2-TagB_at" "AFFX-r2-TagC_at"
> [27] "AFFX-r2-TagD_at" "AFFX-r2-TagE_at"
> [29] "AFFX-r2-TagF_at" "AFFX-r2-TagG_at"
> [31] "AFFX-r2-TagH_at" "AFFX-r2-TagIN-3_at"
> [33] "AFFX-r2-TagIN-5_at" "AFFX-r2-TagIN-M_at"
> [35] "AFFX-r2-TagJ-3_at" "AFFX-r2-TagJ-5_at"
> [37] "AFFX-r2-TagO-3_at" "AFFX-r2-TagO-5_at"
> [39] "AFFX-r2-TagQ-3_at" "AFFX-r2-TagQ-5_at"
>
> So you could either go to the trouble of building and installing a .db
> package for this array, or you could do something like
>
> featureNames(EsetData) <- gsub("_PM","", featureNames(EsetData))
> annotation(EsetData) <- "hgu133plus2.db"
>
> and carry on as before.
>
> Best,
>
> Jim
>
>
>
>  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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>> science.biology.informatics.**conductor<http://news.gmane.org/gmane.science.biology.informatics.conductor>
>>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>
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>

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