Hi All, In the script4exon.R provided with the xps package. There is no indication that you should upload the antigenomi.bgp file. However, the function for RMA claims to use the antigenomic probes. How is this possible? Thank you Addiel

Dear Addiel, The reason is that the antigenomic.bgp file contains redundant information which is already present in the HuEx-1_0-st-v2.r2.pgf file. Simply search the pgf-file for: control->bgp->antigenomic BTW, in function rma() "antigenomic" is only a parameter which is internally used for the mask. Function rma() still uses the PMs only for background correction of exon arrays. Probably I should clarify this issue in the help file. If you want to use antigenomic probes for background correction you need to call function bgcorrect.gc(). 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 1/29/11 1:39 AM, Addiel de Alba wrote: > > Hi All, > > In the script4exon.R provided with the xps package. There is no indication that > you should upload the antigenomi.bgp file. However, the function for RMA claims > to use the antigenomic probes. How is this possible? > > Thank you > > Addiel > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >