
Hi

Thank you very much for your answer.
I will try this and give you the result.

Thank you for your help.

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 <pmonly:epanechnikov> 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
> >
> >
> > _________________________________________________________________
> >
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