[BioC] Package xps: problem with RMA normalization for Human Gene ST 1.0

[cstrato]

Dear Naima,

This problem appears since for na31 Affymetrix has changed something in 
the probeset annotation file, see:
https://www.stat.math.ethz.ch/pipermail/bioconductor/2010-October/035954.html

Sadly, during this time BioC was updated from BioC 2.6 to BioC 2.7, so I 
could only solve the problem for BioC 2.7 in version xps_1.10.1. Thus 
you need either to upgrade to R-2.12.0 or to use the annotation files 
release na30.

Best regards
Christian


On 10/26/10 3:43 PM, Naïma Oumouhou wrote:
>   //
>
> Dear Christian,
> I have a question about the xps package. I’ve installed root and xps,
> I’ve created the root scheme for the HuGene1.0 array and imported the
> CEL files following the example scripts.
> After RMA normalization, I'm missing a lot of probesets. I have got 57
> probesets. I don’t know why.
>
> Thanks for your help.
>
> Naïma
>
> #Step 1
>
> #------
> library("xps")
>
> #Step 2
>
> #------
> libdir<-
> "D:/Naima/CancerMoelleOsseuse_EFS/Analyse_Package_XPS/HGST1/libraryfiles"
>
> anndir<-
> "D:/Naima/CancerMoelleOsseuse_EFS/Analyse_Package_XPS/HGST1/Annotation"
>
> scmdir<-
> "D:/Naima/CancerMoelleOsseuse_EFS/Analyse_Package_XPS/HGST1/Schemes"
>
> scheme.HGST1.na19<-import.exon.scheme("Scheme_Test1_na19",filedir=scmdir,
>
> layoutfile=paste(libdir,"HuGene-1_0-st-v1.r4.clf",sep="/"),
>
> schemefile=paste(libdir,"HuGene-1_0-st-v1.r4.pgf",sep="/"),
>
> probeset=paste(anndir,"HuGene-1_0-st-v1.na31.hg19.probeset.csv",sep="/"),
>
> transcript=paste(anndir,"HuGene-1_0-st-v1.na31.hg19.transcript.csv",sep="/"),verbose=T)
>
>
> #Step 3
>
> #------
>
> scmdir_HGST1<-
> "D:/Naima/CancerMoelleOsseuse_EFS/Analyse_Package_XPS/HGST1/Schemes"
>
> scheme.HGST1<-root.scheme(paste(scmdir_HGST1,"Scheme_Test1_na19.root",sep="/"))
>
> #Step 4
>
> #------
>
> celdir_DataTLSE<-"D:/Naima/CancerMoelleOsseuse_EFS/Analyse_Package_XPS/HGST1/Data_Tlse"
>
> celfiles <-
> c("MGUS6_(HuGene-1_0-st-v1).CEL","MGUS13_(HuGene-1_0-st-v1).CEL","MGUS15_(HuGene-1_0-st-v1).CEL","MGUS17_(HuGene-1_0-st-v1).CEL","MGUS19_(HuGene-1_0-st-v1).CEL",
>
> "MN1_(HuGene-1_0-st-v1).CEL","MN4_(HuGene-1_0-st-v1).CEL","MN5_(HuGene-1_0-st-v1).CEL","MoPur27_(HuGene-1_0-st-v1).CEL","MoPur28_(HuGene-1_0-st-v1).CEL",
>
> "MoPur32_(HuGene-1_0-st-v1).CEL","MYE2_(HuGene-1_0-st-v1).CEL","MYE8d_(HuGene-1_0-st-v1).CEL","MYE9_(HuGene-1_0-st-v1).CEL","MYE12_(HuGene-1_0-st-v1).CEL",
>
> "MYE18_(HuGene-1_0-st-v1).CEL","MYE20_(HuGene-1_0-st-v1).CEL","MYE22_(HuGene-1_0-st-v1).CEL","MYE23_(HuGene-1_0-st-v1).CEL")
>
> celnames<-c("MGUS6","MGUS13","MGUS15","MGUS17","MGUS19","MN1","MN4","MN5","MoPur27","MoPur28","MoPur32","MYE2","MYE8d","MYE9","MYE12",
>
> "MYE18","MYE20","MYE22","MYE23")
>
> scheme.HGST1_CEL<-import.data(scheme.HGST12,"tmpdt_DataHGST1",celdir=celdir_DataTLSE,celfiles=celfiles,celnames=celnames)
>
> data.rma<-rma(scheme.HGST1_CEL,"tmpdt_TestRMA",background="antigenomic",normalize=T,exonlevel="metacore+affx")
>
> expr.rma_HGST1Test<-validData(data.rma)
>
> dim(expr.rma_HGST1Test)
>
> #[1] 57 19
>
>
> #######################################################"
> sessionInfo()
> R version 2.11.1 (2010-05-31)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252
> [3] LC_MONETARY=French_France.1252 LC_NUMERIC=C
> [5] LC_TIME=French_France.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] xps_1.8.3
>
>