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arnaud Le Cavorzin
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110
@arnaud-le-cavorzin-3364
Last seen 10.3 years ago
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_Huextestprobesetnob
ackRMA",background="none",
+ normalize=TRUE,option="probeset",exonlevel="core",verbose=FALSE)
> data.rma=rma(data.huextest,"tmpdt_HuextestRMA",background="antigenom
ic",
+ 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",fi
ledir=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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