Hi there, I have a number of short RNAs that have high homologies to a number of individual probes in the Medicago Affymetrix Genechip (http:// www.affymetrix.com/products/arrays/specific/medicago.affx) I'd like to be able to see for a few hundred probes which individuals, for example Medicago:AFFX-CreX-5_at:587:698, have high fluorescence levels and which do not. I realise binding efficiencies differ for individual probes, but I am only looking for indicative data. Sorry if I am not clear with proper terminology, I've only worked with pre- made gcrma processed data sets before, not individual probes. Cheers, Chris

Hi Chris, If you want probe level expression values, you will need to extract those data from your AffyBatch (probably best after background subtraction and normalization). You can extract e.g., the PM probe values for AFFX-CreX-5_at using the pm() accessor function: pm(abatch, "AFFX-CreX-5_at") HTH, Jim Chris Dawson wrote: > Hi there, > I have a number of short RNAs that have high homologies to a number > of individual probes in the Medicago Affymetrix Genechip (http:// > www.affymetrix.com/products/arrays/specific/medicago.affx) I'd like > to be able to see for a few hundred probes which individuals, for > example Medicago:AFFX-CreX-5_at:587:698, have high fluorescence > levels and which do not. I realise binding efficiencies differ for > individual probes, but I am only looking for indicative data. Sorry > if I am not clear with proper terminology, I've only worked with pre- > made gcrma processed data sets before, not individual probes. > Cheers, > Chris > > _______________________________________________ > 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, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC 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.