Dear all, j'm using the library xps in order to analyse some .cel file from Human Gene 1.0 st. J have the Scheme for the chip and the Root Tree for the Cel files, when J use the RMA method to compute expression levels, in the output file j have only 25927 records instead of 33297 that is the total number of transcript units. J used this instruction data.rma<- rma(data.banfi,"DataRma",filedir=datadir,tmpdir="",background="antigen omic", normalize=T,exonlevel="metacore+affx") Where is the problem? Thank you Annamaria Carissimo -- Ricordate che e' sempre possibile contribuire alla raccolta fondi di Telethon Remember that it is always possible to send your donation Scoprilo alla pagina: http://www.telethon.it/comedonare/default.aspx

Dear Annamaria If you look at the help file ?rma you will see the following: Following exonlevel annotations are valid for whole genome arrays: core: probesets with category "unique", "similar" and "mixed". metacore: probesets with category "unique" only. affx: standard AFFX controls. all: combination of above (including affx) Thus in your case you need to use one of: - exonlevel = "core+affx", or: - exonlevel = "all" For an explanation of the different categories see the README file coming with the HuGene annotation, especially the section on "crosshyb_type". 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 _._._._._._._._._._._._._._._._._._ carissimo at tigem.it wrote: > Dear all, > > j'm using the library xps in order to analyse some .cel file from Human > Gene 1.0 st. > J have the Scheme for the chip and the Root Tree for the Cel files, when J > use the RMA method to compute expression levels, in the output file j have > only 25927 records instead of 33297 that is the total number of > transcript units. > J used this instruction > data.rma<- > rma(data.banfi,"DataRma",filedir=datadir,tmpdir="",background="antig enomic", > normalize=T,exonlevel="metacore+affx") > > Where is the problem? > > Thank you > > Annamaria Carissimo > > > > > -- > Ricordate che e' sempre possibile contribuire alla raccolta fondi di Telethon > Remember that it is always possible to send your donation > > Scoprilo alla pagina: http://www.telethon.it/comedonare/default.aspx > > _______________________________________________ > 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 > > >