Hello, I would really appreciate if somebody could tell whether it is possible to extract PM and MM spot (not probe) intensities from CEL files. A CEL file has X and Y coordinates and mean intensity associated with each of these locations. I think each spot in an Affymetrix array is either a perfect match or mismatch. Although there is a method in the affy package to extract PM and MM values for each probe I found no method to find PM or MM spot intensity from CEL files. Thanking you in advance, Tapan Mehta

Your question is not very clear, but I will assume that what you want to extract are the pixel intensities for each probe (each probe is in only one spot, so AFAIK, these terms are interchangeable), rather than the 75th percentile of these values (the cel file contains the 75th percentile, not the mean value). The short answer is no. The cel file only contains these 75th percentile values. If you want all the pixel intensities for each spot, you need the dat file. Unfortunately, there is no functionality that I know of for extracting these pixel intensities in BioC. The dat file is simply a 16-bit tiff file, so you need some method to place a grid on the image and then extract each pixel intensity value for each spot. Best, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Tapan Mehta <tapmehta@yahoo.com> 11/25/04 12:55 AM >>> Hello, I would really appreciate if somebody could tell whether it is possible to extract PM and MM spot (not probe) intensities from CEL files. A CEL file has X and Y coordinates and mean intensity associated with each of these locations. I think each spot in an Affymetrix array is either a perfect match or mismatch. Although there is a method in the affy package to extract PM and MM values for each probe I found no method to find PM or MM spot intensity from CEL files. Thanking you in advance, Tapan Mehta _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.