Dear all, Does someone has an explanation why Affymetrix has added probesets w/o MMs to the Citrus.CDF file? BTW, I have just uploaded a new version xps_1.4.9 (and xps_1.5.16) to BioC which allows to do "mas5" and "mas5calls" for the Affymetrix Citrus array by simply skipping the probesets w/o MMs. 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 _._._._._._._._._._._._._._._._._._ James W. MacDonald wrote: > Making any changes to mas5calls will be much less trivial than the > background correction, and I don't have the time right now to spend on > that. > > Your best bet is to use rma() and then filter on something like IQR. > See the genefilter package for more options. > > Best, > > Jim > > > > yuduanding wrote: >> >> >> hello Jim: >> >> Sorry too trouble you again.After I installed affy package1.23.6 and >> Biobase 2.5.6 the mas5 problem have solved.But I meet the similar >> problems when run mas5calls and gcrma package on Citrus chips,I think >> problem must be the NA in Citrus Chip,But I can find another way to >> filtering out low quality data. >> >> Here are the partial R codes : >>> library(affy) >>> affydata<-ReadAffy("cp1-a.CEL") >>> affydata >> AffyBatch object >> size of arrays=984x984 features (16 kb) >> cdf=Citrus (30395 affyids) >> number of samples=1 >> number of genes=30395 >> annotation=citrus >> notes= >> >>> mas5.eset<-mas5(affydata) >> background correction: mas PM/MM correction : mas expression values: >> mas background correcting...done. >> 30395 ids to be processed >> #work well!!no problems!! >> >> >>> pa_calls<-mas5calls(affydata) >> Getting probe level data... >> Computing p-values >> Error in FUN(1L[[1L]], ...) : NA/NaN/Inf in foreign function call >> >> >>> gcrma(affydata) >> Adjusting for optical effect.Done. >> Computing affinitiesLoading required package: AnnotationDbi >> Error in matrix(NA, nrow = max(cbind(pmIndex, >> mmIndex)), ncol = 1) :matrix: invalid 'nrow' value (too large or NA) >> >>> sessionInfo() >> R version 2.9.1 (2009-06-26) x86_64-unknown-linux-gnu >> locale: >> LC_CTYPE=zh_CN.UTF-8;LC_NUMERIC=C;LC_TIME=zh_CN.UTF-8;LC_COLLATE=zh _CN.UTF-8;LC_MONETARY=C;LC_MESSAGES=zh_CN.UTF-8;LC_PAPER=zh_CN.UTF-8;L C_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=zh_CN.UTF-8;LC_IDE NTIFICATION=C >> >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> other attached packages: >> [1] citrusprobe_2.4.0 AnnotationDbi_1.6.1 gcrma_2.16.0 [4] >> Biostrings_2.12.8 IRanges_1.2.3 citruscdf_2.4.0 [7] >> affy_1.23.6 Biobase_2.5.6 >> loaded via a namespace (and not attached): >> [1] affyio_1.12.0 DBI_0.2-4 preprocessCore_1.6.0 >> [4] RSQLite_0.7-2 splines_2.9.1 tools_2.9.1 >> Best. >> YuduanDing >> >> RE: >> >> <jmacdon at="" med.umich.edu="">" 2009-09-02 22:56:01 >> Re: RE James about mas5 >> The problem with running mas5 on the citrus chip is that there are 25 >> probesets that don't have any MM probes. Since the MM probes are used >> for both background estimation/subtraction and computation of the >> expression values this will be a problem for these probesets. >> >> I have fixed the error you see in the devel version of affy, so if >> you want to run mas5 on these data you need to upgrade to the devel >> version of R, and then either get the corrected version of affy from >> the svn server, or wait a day or two and use biocLite() to get it. >> The version of the corrected affy package is 1.23.6. >> >> Best, >> >> Jim >> >> >> >> wrote: >> >> >> >> ------------------------------------------------------------------- ----- >> >> _______________________________________________ >> 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 >