Dear Larry, As already mentioned, when using exon arrays I can reproduce your observation. It turns out that for exon arrays I can no longer loop over internal unitIDs, which I had changed correctly for the UniFilter code but forgot to change for the PreFilter code. Thank you for reporting this problem. I have already uploaded the new version xps_1.8.2 to BioC which should be available tomorrow. I must ask users of xps, who are using function "prefilter()" with exon arrays, to upgrade to the new version xps_1.8.2 in order to avoid loosing transcripts/probesets satisfying the prefilter conditions (As mentioned above function "unifilter()" is not affected). I apologize for the inconvenience. Best regards Christian On 6/30/10 10:46 PM, cstrato wrote: > Dear Larry, > > When using the Test3 examples coming with xps I get the following: > > > scheme.test3 <- root.scheme(paste(.path.package("xps"), > "schemes/SchemeTest3.root", sep="/")) > > data.test3 <- root.data(scheme.test3, paste(.path.package("xps"), > "rootdata/DataTest3_cel.root", sep="/")) > > data.rma <- rma(data.test3, "Test3RMA", tmpdir="", > background="pmonly", normalize=TRUE) > > > preflr <- PreFilter(mad = c(0.25)) > > rma.pfr <- prefilter(data.rma, "tmp_prefilter", getwd(), > filter=preflr, minfilters=1, logbase="log2") > Creating new temporary file > </volumes>... > Opening file > </users> in > <read> mode... > Opening file </volumes> in <read> > mode... > Prefilter: <41> genes of <345> genes fulfill filter criteria. > Opening file > </users> in > <read> mode... > Opening file </volumes> in > <read> mode... > Opening file </volumes> in > <read> mode... > Exporting data from tree <prefilter> to file > </volumes>... > > > tmp <- validData(rma.pfr) > > d <- dim(tmp[tmp[, "FLAG"] == 1,]) > > d > [1] 41 2 > > > x <- validData(data.rma) > > x <- log(x)/log(2) > > mads <- apply(x, 1, mad) > > sum(mads > 0.25) > [1] 41 > > As you can see, in both cases I get the same result. > > Did you copy/paste the code you have sent? > Could you give the sessionInfo() so that I know which version of xps you > are using? > Could you please run this example and tell me if your result differs > from the one above? > Furthermore, which array type are you using? > > Best regards > Christian > _._._._._._._._._._._._._._._._._._ > C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a > V.i.e.n.n.a A.u.s.t.r.i.a > e.m.a.i.l: cstrato at aon.at > _._._._._._._._._._._._._._._._._._ > > > On 6/30/10 7:01 PM, Larry N. Singh wrote: >> >> Hi everyone, >> >> I'm having some issues with the madFilter in xps. Please see below: >> >> # Please note I've already loaded the RMA data in data.rma >> preflr<- Prefilter(mad = c(0.25)) >> rma.pfr<- prefilter(data.rma, "tmp_prefilter", getwd(), >> filter=preflr, minfilters=1, logbase="log2") >> >> tmp<- validData(rma.pfr) >> d<- dim(tmp(tmp[, "FLAG"] == 1,]) >> >>> d >> 208 2 >> >> #### BUT >> >> x<- validData(data.rma) >> x<- log(x)/log(2) >> mads<- apply(x, 1, mad) >> >>> sum(mads> 0.25) >> [1] 3641 >> >> I don't get the same numbers for MAD filtering. >> Can someone please tell me what I'm missing here? >> >> Thank you kindly for any help. >> -Larry. >> >> _______________________________________________ >> 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 >> > > _______________________________________________ > 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 >