
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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