[BioC] Xps package : errors and RMA difference with Partek GS

[cstrato]

Dear Arnaud,

The error you get does only appear on Windows, since MS VC++ requires 
every C function used to be listed in an Export Definition File 
"xps.def". Since I have added this function later and do use WinXP only 
for testing purposes, I have forgotten to add function "MetaProbesets".

I have just uploaded a new version xps_1.2.8 to BioC which adds this 
function to xps.def.
You should be able to download the new version in the next one or two days.

Thank you for reporting this error. I am sorry for the inconvenience.

Best regards
Christian


arnaud Le Cavorzin wrote:
> 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 at aon.at
> > To: arnaudlc at msn.com
> > CC: bioconductor at stat.math.ethz.ch; delphine.rossille at 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
> > >
> > >
> > > _________________________________________________________________
> > >
> > > ? Lancez-vous !
> > >
> > > [[alternative HTML version deleted]]
> > >
> > >
> > > 
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