I am having problem with updating affy package, getting message: cannot open compressed file 'C:/PROGRA~1/R/R-22~1.0DE/library/affy/R/all.rda' Error in library(affy) : .First.lib failed for 'affy' (run on windowsxp prof. R 2.2.0 dev and all packages are dev) Running simpleaffy package I get message: raw.data <- read.affy("covdesc.txt") #read data in working directory > x.rma <- call.exprs(raw.data, "rma") # Creates expression values Background correcting Normalizing Calculating Expression > write.exprs(x.rma, file="rma_affy_all.txt") > results <- pairwise.comparison(x.rma, "animal", c("1", "2"), raw.data) Getting probe level data... Computing p-values Error in as.double(pms[, x]) : subscript out of bounds Thanks for help. Narendra Narendra Kaushik School of Biosciences, University of Cardiff, Cardiff CF10 3US kaushiknk at cardiff.ac.uk