[BioC] RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene

[Henrik Bengtsson]

Hi.

On Fri, Feb 26, 2010 at 5:38 PM, Mikhail Pachkov <pachkov at gmail.com> wrote:
> Dear Henrik and Benilton,
>
> Thank you for explanations. I have tried plotDensity with types="pm"
> and results now look consistent.

Great.  There is almost always a simple explanation to everything.

> I have also found that oligo::rma perform summarization to the
> *probeset* level not probe level. I guess that is why my plots looked
> so different. I have used rma.background.correct from preprocessCore
> and now data look close to each other.

Good.

>
> I would like to ask Henrik, how can I get probe id list within
> aroma.affymetrix in order to print table of probe id and corresponding
> expression values?

This is really a question for the aroma.affymetrix mailing list,

  http://www.aroma-project.org/forum

and it has been asked and answered there before.  I make an exception
and answer it here.  First, you probably mean "probset id" not "probe
id" (big difference and there is no such thing as "probe id").
Second, in the aroma.affymetrix world we use the term "unit names"
instead of "probeset id" (there is good reason for this, but I won't
explain it here).  You are probably looking for what
extractDataFrame() provides, cf.

  http://www.aroma-project.org/howtos/extractDataFrame

Make sure to look through http://www.aroma-project.org/ - that's the
number one source for all documentation of aroma.affymetrix and
friends.

Hope this helps

Henrik

/Henrik

>
> Kind regards,
>
> Mikhail
>
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