Hi I have tried to create a .mps file with xps. But I have got an error, in french "Erreur dans .C("MetaProbesets", as.character(schemefile), as.character(infile), : le nom C de symbole "MetaProbesets" est introuvable dans la DLL pour le package "xps" " That means that there is an error with the name C of symbol MetaProbesets is missing into the ddl for the package xps. I don't understand what it mean, can you help me about this? The script used : > xps.rma=validData(data.rma) > writeLines(rownames(xps.rma),"core.txt") > metaProbesets(scheme.huex10stv2r2,"core.txt","coreList.mps", + exonlevel="core") (I have performed a RMA with background="antigenomic",option="transcript" and exonlevel="core" before this, for the comparison with APT and Partek GS) Thank you Best regards Arnaud > Date: Sat, 28 Mar 2009 23:03:21 +0100 > From: cstrato@aon.at > To: arnaudlc@msn.com > CC: bioconductor@stat.math.ethz.ch; delphine.rossille@chu-rennes.fr > Subject: Re: [BioC] Xps package : errors and RMA difference with Partek GS > > Dear Arnaud, > > Regarding the problem with "bgcorrect.rma()": > Currently function "bgcorrect.rma()" works only with expression arrays, > I will update it in the next version. > At the moment you need to use the general function "bgcorrect()" with > the correct settings. > > Thus if you want to compute RMA stepwise you need to do: > ## 1.step: background - rma > data.bg.rma <- bgcorrect(data.exon, "ExonRMABgrd", filedir=datdir, > method="rma", select="antigenomic", option="pmonly:epanechnikov", > params=c(16384), exonlevel="core") > > ## 2.step: normalization - quantile > data.qu.rma <- normalize.quantiles(data.bg.rma, "ExonRMANorm", > filedir=datdir , exonlevel="core") > > ## 3.step: summarization - medpol > data.mp.rma <- summarize.rma(data.qu.rma, "ExonRMASum", filedir=datdir, > exonlevel="core") > > > This will give the same expression levels as using function "rma()" > directly: > ## compute rma: > data.rma <- rma(data.exon, "ExonRMAcore", filedir=datdir, > background="antigenomic", > normalize=T, option="transcript", exonlevel="core") > > > Alternatively you can use function "express()" to compute RMA: > a, stepwise: > ## 1.step: background - rma > expr.bg.rma <- express(data.exon, "ExonExprsBgrd", filedir=datdir, > tmpdir="", > bgcorrect.method="rma", bgcorrect.select="antigenomic", > bgcorrect.option="pmonly:epanechnikov", bgcorrect.params=c(16384), > exonlevel="core") > > ## 2.step: normalization - quantile > expr.qu.rma <- express(expr.bg.rma, "ExonExprsNorm", filedir=datdir, > tmpdir="", > normalize.method="quantile", normalize.select="pmonly", > normalize.option="transcript:together:none", normalize.logbase="0", > normalize.params=c(0.0), exonlevel="core") > > ## 3.step: summarization - medpol > expr.mp.rma <- express(expr.qu.rma, "ExonExprsSum", filedir=datdir, > tmpdir="", > summarize.method="medianpolish", summarize.select="pmonly", > summarize.option="transcript", summarize.logbase="log2", > summarize.params=c(10, 0.01, 1.0), exonlevel="core") > > > b, with a single call to express() > expr.rma <- express(data.exon, "ExonExprs", filedir=datdir, tmpdir="", > bgcorrect.method="rma", bgcorrect.select="antigenomic", > bgcorrect.option="pmonly:epanechnikov", bgcorrect.params=c(16384), > normalize.method="quantile", normalize.select="pmonly", > normalize.option="transcript:together:none", normalize.logbase="0", > normalize.params=c(0.0), summarize.method="medianpolish", > summarize.select="pmonly", summarize.option="transcript", > summarize.logbase="log2", summarize.params=c(10, 0.01, 1.0), > exonlevel="core") > > > I hope that these examples help you to use functions bgcorrect(), > normalize.quantiles(), summarize.rma() and express(). > > Best regards > Christian > > > arnaud Le Cavorzin wrote: > > Hi all. > > > > I'm a new user of the xps package and I have some questions about it and some problems. > > > > I use xps package for analysing exon arrays (using Affymetrix Human Exon 1.0 ST Arrays), and I try to compare the results with the results obtained with Partek GS. > > > > So for that in R I import .CEL files and perform a RMA (using function rma with xps). I have no problem with this step, it works but I don't obtain the same results with Partek. > > I have tried different options for rma (xps package) and for Partek (changing option=transcript or probeset, exonlevel=core or metacore in xps for example, and do the same thing in Partek) but the results are always differents. > > > > When I import the data from the .CEL files, all is ok, I have the same results with xps and Partek. But whenever I try a normalization (RMA) the results are different from the two softwares. > > I have done for example : > > > > > >> data.probesetnoback.rma=rma(data.huextest,"tmpdt_HuextestprobesetnobackRMA",background="none", > >> > > + normalize=TRUE,option="probeset",exonlevel="core",verbose=FALSE) > > > >> data.rma=rma(data.huextest,"tmpdt_HuextestRMA",background="antigenomic", > >> > > + normalize=TRUE,option="probeset",exonlevel="core",verbose=FALSE) > > > >> data.metacore.rma=rma(data.huextest,"tmpdt_HuextestprobesetnobackRMA",background="antigenomic", > >> > > + normalize=TRUE,option="probeset",exonlevel="metacore",verbose=FALSE) > > > > > > I have also tried with the xps package to perform a background correction first, after a quantile normalization and finally a summarization for compare step by step with Partek but it doesn't work. > > > > I can't perform bgcorrect without error, like for example : > > > > > >> data.qu.rma=bgcorrect.rma(data.huextest,"tmpdt_HuextestbgqumpRMA",filedir=getwd(), > >> > > + tmpdir="",exonlevel="core",verbose=FALSE) > > Erreur dans .local(object, ...) : error in function ‘BgCorrect’ > > > >> traceback() > >> > > 6: stop(paste("error in function", sQuote("BgCorrect"))) > > 5: .local(object, ...) > > 4: xpsBgCorrect(xps.data, filename = filename, filedir = filedir, > > tmpdir = tmpdir, update = update, select = select, method = method, > > option = option, exonlevel = exonlevel, params = params, > > verbose = verbose) > > 3: xpsBgCorrect(xps.data, filename = filename, filedir = filedir, > > tmpdir = tmpdir, update = update, select = select, method = method, > > option = option, exonlevel = exonlevel, params = params, > > verbose = verbose) > > 2: bgcorrect(xps.data, filename = filename, filedir = filedir, tmpdir = tmpdir, > > update = update, select = "none", method = "rma", option = "pmonly:epanechnikov", > > exonlevel = exonlevel, params = c(16384), verbose = verbose) > > 1: bgcorrect.rma(data.huextest, "tmpdt_HuextestbgqumpRMA", filedir = getwd(), > > tmpdir = "", exonlevel = "core", verbose = FALSE) > > > >> data.bg.rma=bgcorrect(data.huextest,"tmpdt_HuextestbgqumpRMA", filedir = getwd(), tmpdir = "", select="none",method="rma",option="none",exonlevel = "core", verbose = FALSE) > >> > > Erreur dans .local(object, ...) : empty parameter list ‘params’ > > De plus : Warning message: > > In .local(object, ...) : > > ‘option’ is different from for rma > > > > > > If I perform a normalization.quantiles without performing a bgcorrect it doesn't work, I obtain 0 for all of the values. > > And summarization give the same kind of error than bgcorrect. > > > > Therefore my questions : > > > > Why xps pakage and R don't give the same results using the same setup options? > > What does exactly xps when performing a RMA? A bgcorrect? A normalization? > > > > Thanks for your answer > > Best regards > > > > Arnaud > > > > > > _________________________________________________________________ > > > > ? Lancez-vous ! > > > > [[alternative HTML version deleted]] > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > _________________________________________________________________ clics ! [[alternative HTML version deleted]]