Dear Jorge, Please see the vignette "APTvsXPS.pdf" for a comparison between APT and xps, and see Figure 25 for the reason why xps did not implement PLIER. I do not think that you can import the APT output into xps, at least not from within R (although it might be possible from C++, but I would have to check). Best regards Christian On 6/2/12 5:20 PM, Jorge Mir? wrote: > Hi Christian, > > Oh, very nice. Is there any way of running PLIER in XPS too? Or is there > any possibility of producing the expressions with Affymetrix APT and > then use the output files in XPS to do a quality analysis within XPS? > > Kindly > Jorge > > On Sat, Jun 2, 2012 at 5:14 PM, cstrato <cstrato at="" aon.at=""> <mailto:cstrato at="" aon.at="">> wrote: > > Dear Jorge, > > You can preprocess both, RaExon and RaGene 1.0 ST arrays, at the > probeset and the gene level, simply set the option to either > option="probeset" or to option="transcript", e.g.: > > data.rma <- rma(data.genome ,"RaGeneRMAMetacore", filedir=datdir > background="antigenomic", normalize=TRUE, option="transcript", > exonlevel="metacore+affx") > > See the help file ?rma. > > For further examples see the scripts "script4exon.R" and > "script4xps.R" in the xps/examples directory. See also script > "script4schemes.R" how to create the scheme for the RaGene array. > > 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 <http: aon.at=""> > _._._._._._._._._._._._._._._.___._._ > > > > > > On 6/2/12 3:02 AM, Jorge Mir? [guest] wrote: > > > I was wondering if there is some way of getting the XPS package > working at gene level as I need to get the gene expression from > some Rat Gene chips (RaGene 1.0 ST r4)that I will analyze. > > I tried to use the Affy package before but as far as I > understand they need .CDF file to get working and I only have > CLF and PBG files for my chips. > > Kind regards > Jorge > > -- output of sessionInfo(): > > - > > -- > Sent via the guest posting facility at bioconductor.org > <http: bioconductor.org="">. > > _________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/__listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: > http://news.gmane.org/gmane.__science.biology.informatics.__conductor > <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > >