I am migrating from affymetrix apt-probeset-summarize to XPS. How do I get expression values via XPS corresponding to the following apt-probeset-summarize options ? 1) "rma-bg,quant-norm.sketch=-1.usepm=true.bioc=true,pm-only,med- polish" 2) "quant-norm.sketch=-1.bioc=true,pm-only,plier" 3) "quant-norm.sketch=-1.bioc=true,pm-gcbg,plier" 4) "pm-only,dabg" 5) "quant-norm.sketch=-1.bioc=true,pm-only,iter-plier" 6) "quant-norm.sketch=-1.bioc=true,pm-gcbg,iter-plier"

Hi, Please have a look at vignette "APTvsXPS.pdf" and the corresponding source code which you can find in "../xps/examples/script4xps2apt.R". For rma you can use function "rma()", for dabg use function "dabg()". Please note that "plier" is not supported. 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 _._._._._._._._._._._._._._._._._._ Daren Tan wrote: > I am migrating from affymetrix apt-probeset-summarize to XPS. How do I > get expression values via XPS corresponding to the following > apt-probeset-summarize options ? > > 1) "rma-bg,quant-norm.sketch=-1.usepm=true.bioc=true,pm-only,med- polish" > 2) "quant-norm.sketch=-1.bioc=true,pm-only,plier" > 3) "quant-norm.sketch=-1.bioc=true,pm-gcbg,plier" > 4) "pm-only,dabg" > 5) "quant-norm.sketch=-1.bioc=true,pm-only,iter-plier" > 6) "quant-norm.sketch=-1.bioc=true,pm-gcbg,iter-plier" > > _______________________________________________ > 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 > > >