[BioC] mas5calls

Arne.Muller at aventis.com Arne.Muller at aventis.com
Mon Oct 27 15:54:23 MET 2003


since recently there's the affy package offers the mas5calls fucntion to get
the P, A or M calls for a summarized probeset.

The usual processing protocol that I use is:

1. read cel file
2. bg correct
3. normalize
4. pm correct
5. summarize

Where would I stick in the mas5calls? I assume this would be between steps 2
and 3 (i.e. before normalization), but it could also be after normalization
or even after pm correct. I'd be interested in your comments.

I'm currently processing some chips from different experimental batches that
have (depending on the batch) a shift in intensities with one batch also
having more present genes (as determined by  the affy .DAT files) than the
other. For this situation I could imagine to use the mas5calls *after*
normalization to get a "faire" call (i.e. what's called 'P' on one chip
should ideally also be called 'P' on the other chip even though the
intensities are quite a lot lower).

	kind regards + thanks for your comments,


Arne Muller, Ph.D.
Aventis Pharma, Drug Safety Evaluation
13 quai Jules Guesde
94403 Vitry-sur-Seine CEDEX, FRANCE
phone: +33-(0)1589-32896
fax  : +33-(0)1589-38197
email: arne.muller at aventis.com

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