[BioC] when to call pmcorrect in affy

Ben Bolstad bolstad at stat.berkeley.edu
Thu Apr 22 19:19:18 CEST 2004

In general you'd apply the background correction function to an
affybatch, to get a bg corrected affybatch. Then send this to a
normaliation routine and so on .... 

For the case that you are asking for no "pmcorrection" is needed . The
recommended way of getting what you want is mentioned on:


"If you are interested in applying the RMA preprocessing to just the PM
probes of an affybatch Data. You might find the following code slightly
more efficient than applying the standard operations
bg.correct(),normalize() to an affybatch. 

my.PM <- apply(pm(Data), 2, bg.adjust)
my.PM <- normalize.quantiles(my.PM)"

On Thu, 2004-04-22 at 10:05, Arne.Muller at aventis.com wrote:
> Hello,
> when processing an affybatch by performing all steps "manually" (i.e. not using expresso or justRMA), when do I call pmcorret?
> does this order make sense?
> 1. bgcorrect (rma)
> 2. normalize (quantiles)
> 3. pmcorrect (pmonly)
>  ... no summary!
> In this case (since I'm using rma) do I have to take care that I remove the MM intensities from the affybatch before passing the bgcorrected affybatch to the normalization (because on the PMs were corrected)?
> Basically I'd just like to skip the last step the "summary" to finally have a matrix with the probe insensities (and not the summarized *probeset* intensities). justMA cannot leave out the summary step, can it?
> 	kind regards + thanks for your comments,
> 	Arne
> --
> Arne Muller, Ph.D.
> Toxicogenomics, Aventis Pharma
> arne dot muller domain=aventis com
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Ben Bolstad <bolstad at stat.berkeley.edu>

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