I want to generate some quality control plots for Affymetrix arrays (initially bovine and Arabidopsis). I'd like to know more about the layout of probes on the array. For instance, when I get the pm and mm probes separately, the number returned is different from that returned by intensity(), why is this?: > dim(pm(AffyBatch))[1] + dim(mm(AffyBatch))[1] [1] 531254 > dim(intensity(AffyBatch))[1] [1] 535824 Also, there doesn't appear to be any PM or MM probes on the outside edge of the array, i.e. column/row 1 and n (where n is the size of the array) - is there any reason for this? What are the probes on the outside edge supposed to measure? Cheers, Nathan ------------------------------------------------------------- Dr. Nathan S. Watson-Haigh (publish under Haigh, N.S.) OCE Post Doctoral Fellow CSIRO Livestock Industries J M Rendel Laboratory Rockhampton QLD 4701 Tel: +61 (0)7 4923 8121 Australia Fax: +61 (0)7 4923 8222

There are several "QC" probes on an Affy array. QC is a term Affy uses and it is (I would say) a bit different than what most stat people would think of. Basically, QC probes contains really bright probes that are used for gridding the image. The QC probes also contains other types of probes. These probes are typically at the edge of the array, although for larger arrays they could be all over. You should read up a bit on this. I recommend reading the affymetrix file format specifications. Also take a look at an ASCII CDF file so you get an idea about what goes on. affxparser has special routines for reading these QC probes and I know you can do it with affyio as well. No-one uses them for anything, besides the images processing - at least as far as I know. Kasper On Jul 17, 2008, at 9:56 PM, <nathan.watson-haigh at="" csiro.au=""> <nathan .watson-haigh="" at="" csiro.au=""> wrote: > I want to generate some quality control plots for Affymetrix arrays > (initially bovine and Arabidopsis). > > I'd like to know more about the layout of probes on the array. For > instance, when I get the pm and mm probes separately, the number > returned is different from that returned by intensity(), why is this?: > >> dim(pm(AffyBatch))[1] + dim(mm(AffyBatch))[1] > [1] 531254 >> dim(intensity(AffyBatch))[1] > [1] 535824 > > Also, there doesn't appear to be any PM or MM probes on the outside > edge > of the array, i.e. column/row 1 and n (where n is the size of the > array) > - is there any reason for this? What are the probes on the outside > edge > supposed to measure? > > Cheers, > Nathan > > > ------------------------------------------------------------- > Dr. Nathan S. Watson-Haigh (publish under Haigh, N.S.) > OCE Post Doctoral Fellow > CSIRO Livestock Industries > J M Rendel Laboratory > Rockhampton > QLD 4701 Tel: +61 (0)7 4923 8121 > Australia Fax: +61 (0)7 4923 8222 > > _______________________________________________ > 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