The summarization step of RMA (which is a core part of the algorithm) does not make sense unless you actually have several probes to summarize. Kasper On Oct 29, 2007, at 6:44 AM, James W. MacDonald wrote: > Hi Alice, > > Johnstone, Alice wrote: >> Hi, >> Is it possible to apply the transformations used on the probesets to >> individual probe expression? Such as RMA and fitting to a lm to >> obtain >> your list of probesets of interest. Then potentially looking at >> individual probe expression levels across samples for all 11 >> probes of >> that probeset? (but normalized across samples to enable greater >> accuracy of the eyeball-o-meter) >> The reason behind this pondering is to investigate further transcript >> variant effects, and also to better match qpcr investigations to the >> location of the probe which shows the greatest change... > > If I understand you correctly, you want to go back to the > background-corrected, normalized pm data for certain probesets to see > the contribution of individual probes. > > This shouldn't be difficult. > > dat <- ReadAffy() > dat <- bg.correct.rma(dat) ## background corrected > dat <- normalize.AffyBatch.quantiles(dat) > > Now you can look at individual probesets using > > pm(dat, 'a.probeset.id') > > Best, > > Jim > > >> Cheers, >> Alice >> >> >> P Think before you print >> This e-mail transmission and any attachments that accompany it may >> contain information that is privileged, confidential or otherwise >> exempt from disclosure under applicable law and is intended solely >> for the use of the individual(s) to whom it was intended to be >> addressed. >> If you have received this e-mail by mistake, or you are not the >> intended recipient, any disclosure, dissemination, distribution, >> copying or other use or retention of this communication or its >> substance is prohibited. If you have received this communication >> in error, please immediately reply to the author via e-mail that >> you received this message by mistake and also permanently delete >> the original and all copies of this e-mail and any attachments >> from your computer. Thank you. >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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