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

[cstrato]

Dear Arnaud,

I have extensively compared the results obtained with "xps" to the 
results obtained with the "Affymetrix Power Tools" (APT) which you can 
freely download from the Affymetrix web-site. Thus I would suggest to 
have a look at the vignette "APTvsXPS.pdf" and the corresponding source 
code which you can find in "../xps/examples/script4xps2apt.R". As you 
will see, for expression arrays the results obtained for rma are 
identical while there are some minor differences for exon arrays; the 
reason for these minor differences are explained in the vignette.

As for Partek I would suggest that you compare the results obtained with 
Partek to the results obtained with APT. If the results are identical 
then the differences are due to the differences explained in the vignette.

Please note that in order to compare the results obtained with xps to 
the results obtained with APT (and with Partek) you need to create a 
meta-probeset file "metaprobeset.mps" (similar to the Affymetrix file 
"HuEx-1_0-st-v2.r2.dt1.hg18.core.mps") using function "metaProbesets()" 
(see help ?metaProbesets).

In package "xps" function "rma()" does the same as in package "affy", 
see the comparison of the expression arrays in vignette "APTvsXPS.pdf".

Regarding the problem with "bgcorrect.rma()" I need to investigate.

Best regards
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a
V.i.e.n.n.a A.u.s.t.r.i.a
e.m.a.i.l: cstrato at aon.at
_._._._._._._._._._._._._._._._._._


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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