Hi, I am trying to use the qc function in the simpleaffy package to generate those qc metrics for a bunch of cel files in U133A, but I need to use a different cdf file, not the Affy CDF. Below is the code library(simpleaffy) cel.path <- "C:\Cel" fn <- list.celfiles(cel.path, full.name = T) raw.data <- ReadAffy(filenames = fn,cdfname = "hgu133ahsentrezg") x.mas5 <- call.exprs(raw.data,"mas5",sc = 100) qcmas5 <- qc(raw.data,x.mas5) Everything runs smoothly except the last line, it has the following warning message: Warning message: In qc.affy(unnormalised, ...) : CDF Environment name ' hgu133acdf ' does not match cdfname ' hgu133ahsentrezgcdf ' Is this problem negligible? or it is serious? I've looked into the qc function and it does not seem to have an argument that allows you to specify cdfname. Thanks, -James