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

[cstrato]

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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