Hello James, I am surprised to see that - apparently - simpleaffy detects that another chip is provided than returned via the 'annotation(raw.data)' function. Such a message would worry me indeed. Having said this: why would you want to perform QC utilizing the MBNI Custom CDF? The Custom CDF won't 'magically' improve bad quality arrays! In other words: performing QC utilizing the (default) Affymetrix CDF is just fine to assess thequality of your arrays. Regards, Dr. Philip de Groot Ph.D. Bioinformatics Researcher Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism & Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786 F: +31-317-483342 E-mail: Philip.deGroot at wur.nl <mailto:philip.degroot at="" wur.nl=""> Internet: http://www.nutrigenomicsconsortium.nl <http: www.nutrigenomicsconsortium.nl=""/> http://humannutrition.wur.nl <http: humannutrition.wur.nl=""/> https://madmax.bioinformatics.nl <https: madmax.bioinformatics.nl=""/> ________________________________ From: James Anderson [mailto:janderson_net@yahoo.com] Sent: Wed 31-3-2010 15:31 To: bioconductor at stat.math.ethz.ch Subject: [BioC] question regarding qc function in simpleaffy package 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