[BioC] rma normalization and more

Ben Bolstad bmb at bmbolstad.com
Fri Nov 23 22:59:47 CET 2007

Depending on how or what your data is you may or may not be able to do
the full RMA. Since you don't seem to have CEL files I am guessing that
you may not have Affymetrix data, and then the full algorithm might not
be applicable. That said all the parts are exposed in one way or

For the background correction, see

bg.adjust() in affy

for quantile normalization see 

normalize.quantiles() in preprocessCore

For the median polish summarization, see

subColSummarizeMedianpolish() in preprocessCore

On Fri, 2007-11-23 at 16:37 -0500, Weiwei Shi wrote:
> Hi there:
> suppose i have some arrays and their log10(intensities) have been made
> into a data.frame of probe X sample;
> I am wondering for that case, is there some normalization function
> available in BioC for that? I do not have other info like background
> info so I think I cannot run something like justRMA since it is a
> wrapper. My question is, if I want to do rma normalization only, is
> there a way to do that?
> I feel sometimes it is good to have a wrapper function; but sometimes
> I would rather have some basic functions so that I can customerize the
> pipeline.
> Best,

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