Hi I have got different GCRMA results on Windows and Linux. Basicly I run the standart GCRMA on three replicate U133A chips and get correlation 0.86 between the windows and linux results. I have the same package versions on linux and windows: > package.version("gcrma") [1] "1.1.3" > package.version("hgu133acdf") [1] "1.4.3" > package.version("hgu133aprobe") [1] "1.0" > On windows > R.Version() $platform [1] "i386-pc-mingw32" ....... >data <- ReadAffy(filenames=c(".............../GP00067.CEL","............/GP000 25.CEL","....../GP00057.CEL"),phenoData="PC3.pdata") > eset.gcrma <- gcrma(data) Computing affinities.Done. Adjusting for optical effect...Done. Adjusting for non-specific binding...Done. Normalizing Calculating Expression >write.table(exprs(eset.gcrma),file="PC3.eset.gcrma",quote=FALSE,sep=" \t", row.names = TRUE, col.names = TRUE) copy PC3.eset.gcrma to PC3.eset.w.gcrma on Linux on linux > package.version("gcrma") [1] "1.1.3" > > R.Version() $platform [1] "i686-pc-linux-gnu" ........ > data <- ReadAffy(filenames=c("......./GP00067.CEL","..../GP00025.CEL","...../G P00057.CEL"),phenoData="PC3.pdata") > eset.gcrma <- gcrma(data) Computing affinities.Done. Adjusting for optical effect...Done. Adjusting for non-specific binding...Done. Normalizing Calculating Expression #read the windows expression values > eset.gcrm.w <- read.exprSet("PC3.eset.w.gcrma") > cor(exprs(eset.gcrma),exprs(eset.gcrm.w)) GP00067.CEL GP00025.CEL GP00057.CEL GP00067.CEL 0.8633871 0.8613008 0.8612103 GP00025.CEL 0.8629481 0.8615257 0.8608711 GP00057.CEL 0.8639332 0.8619907 0.8625088 #just correlation function check > cor(exprs(eset.gcrma),exprs(eset.gcrma)) GP00067.CEL GP00025.CEL GP00057.CEL GP00067.CEL 1.000000 0.999486 0.999442 GP00025.CEL 0.999486 1.000000 0.999133 GP00057.CEL 0.999442 0.999133 1.000000 Alspn u133B chip result are different.Thanks in advance for any suggestions Vladimir [[alternative HTML version deleted]]