// 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/libraryfil es" 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=scmd ir, 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","M N5","MoPur27","MoPur28","MoPur32","MYE2","MYE8d","MYE9","MYE12", "MYE18","MYE20","MYE22","MYE23") scheme.HGST1_CEL<-import.data(scheme.HGST12,"tmpdt_DataHGST1",celdir=c eldir_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 [[alternative HTML version deleted]]