Dear list, I have a short question on read.probematrix(). I use an Affymetrix hgu133plus2 chip. It has 1164 rows and 1164 columns. Thus I expect 1354896 (=1164*1164) messured intensity points. But reading a cel-file I receive 2 (pm and mm) * 604258 = 1208516 entries. The difference is 146380. Even if I take the QC into account I'm slightly confused. It would be kind if you helped me. Greetings Gunther

Gunther H?ning wrote: > Dear list, > > I have a short question on read.probematrix(). > I use an Affymetrix hgu133plus2 chip. It has 1164 rows and 1164 columns. > Thus I expect 1354896 (=1164*1164) messured intensity points. But reading a > cel-file I receive 2 (pm and mm) * 604258 = 1208516 entries. > The difference is 146380. Even if I take the QC into account I'm slightly > confused. If you look at the .tiff file in GCOS you will see that there is a 'checkerboard' of probes that go completely around the outside of the chip. These are used by the affy software to align the scanner, and are scanned, but are neither QC nor expression measuring probes. I believe these make up most of your missing probes. Best, Jim > > It would be kind if you helped me. > > Greetings > > Gunther > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.