[BioC] mas5calls

[Rafael A. Irizarry]

if you want to reproduce affymetrix's calls you should do it after 1. 
results may improve if you do it after 3 but you certainly want to do it 
before 4.


On 
Mon, 27 Oct 2003 Arne.Muller at aventis.com wrote:

> Hello,
> 
> 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
> 
> --
> 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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