[BioC] subtractmm problem in "affy"

[Anja von Heydebreck]

I'm wondering whether a problem with Ben's suggestion might be that in
expresso, the pmcorrect step is applied after background correction (and
normalization), and the RMA bg correction is applied to the PM
intensities only. So, as far as I understand, by choosing pmcorrect.method
other than "pmonly" together with "bgcorrect.method="rma", one would
subtract not-bgcorrected MM intensities from bgcorrected PM intensities.

> Date: Wed, 21 Apr 2004 13:55:12 -0700
> From: Ben Bolstad <bolstad at stat.berkeley.edu>
> Subject: Re: [BioC] subtractmm problem in "affy"
> To: "PARK,CHRISTOPHER CHANGSUN" <ccpark at ucla.edu>
> Cc: bioconductor at stat.math.ethz.ch
> Message-ID: <1082580912.1635.56.camel at bmbbox.dyndns.org>
> Content-Type: text/plain
>
> the problem is that the medianpolish summarization method takes a log2
> transformation of the data. if you use subtractmm  there is the
> possibility of gettting negatives. Perhaps you want to use
>
> pmcorrect.method="mas"
>
> which will used a modified version of MM. This will not give you the
> same problem of NA.
>
>
> On Wed, 2004-04-21 at 13:49, PARK,CHRISTOPHER CHANGSUN wrote:
> > Hi all,
> >
> > I am trying to normalize microarray data using the subtractmm method using
> > the "affy" library.
> >
> > The following is my R script:
> >
> > set.seed(123)
> > library(affy)
> > Data <- ReadAffy()
> > eset<-expresso(Data,bgcorrect.method="rma",
> > normalize.method="quantiles",
> > pmcorrect.method="subtractmm",
> > summary.method="medianpolish")
> > write.exprs(eset,file="subtractmm_data.txt")
> >
> > During the normalization, I encounter the following error message:
> >
> > Error in if (converged) break : missing value where TRUE/FALSE needed
> > In addition: Warning message:
> > NaNs produced in: log(x, base)
> > ...
> >
> > The processed data is a grid of NA's.
> >

Best,
Anja

--
Dr. Anja von Heydebreck
Department of Bio- and Chemoinformatics
Merck KGaA
64271 Darmstadt, Germany
Phone: ++49-6151-723235
Fax:   ++49-6151-723329
anja.von.heydebreck at merck.de