Hi Julie, Julie Dickerson wrote: >>Hi Julie, >> >>Julie Dickerson wrote: >> >>>I am trying to figure out how to get the information about the number >>>of >>>stat_pairs used in the MAS5 computations for each probe set. THis >>>information does not appear to be in the exprsSet class. Is it an >>>intermediate value from one of the normalization steps? Does anyone >>>know >>>how to pull out this information? >> >>What exactly is a stat_pair? >> > > > According to the Affy literature: > Stat Pair: The number of probe pairs available for this probe set > Stat Pairs Used: the number of probe pairs used to make a detection call > for a probe set. > > The first one can, of course, be found from the cdf file with a little > work. It is that Stat Pairs Used that I cannot figure out how to get. Well, you could do it, but it might take a bit of work. It appears to me from the C code https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affy/src/m as5calls.c that the stat pairs used is determined solely by saturation of the MM probe(s) in a probeset. I think the 'stock' setting for saturation is 46000, so you could do something like this: abatch <- ReadAffy() mms <- mm(abatch, LISTRUE = TRUE) mm.counts <- t(sapply(mms, function(x) apply(x, 2, function(y) sum(y > 46000)))) Then you will have a matrix with the stat pairs used for each Affy ID and each chip. HTH, Jim > > > -- 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.