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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.

Naļma

#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



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