[BioC] gcrma

[Jenny Drnevich]

Here is one solution to do it piece by piece, although not in expresso:

First, modify the gcrma function to just do the background correction. Type:

 > mygcrma <- edit(gcrma)

and change the last line to read:

return(object)

Then call:

 >gc.affybatch <- mygcrma(raw.affybatch)

and you'll get an affybatch object with GC background corrected data.

You can then do quantile normalization on this (or any other affybatch) by 
simply calling:

 > gcnorm.affybatch <- normalize(gc.affybatch)

To just do the summarization on any affybatch, try:

gcnorm.eset <- rma(gcnorm.affybatch, background=F, normalize=F)

You can also turn off background correction and normalization in expresso, 
but the rma routine is faster. I don't think you can turn off summarization 
in expresso - see ?expresso.

Cheers,
Jenny


At 05:30 AM 11/1/2005, Bettina Harr wrote:
>dear list,
>
>I would like to decompose the function 'gcrma' into its individual
>elements using the function 'expresso'. Does anyone know which of the
>individual methods (i.e. background correction, pm correction,
>normalization and summarization) I have to use in expresso to get gcrma
>as a result?
>
>Thanks
>
>Tina
>
>_________________________________________________
>
>Bettina Harr
>Research Group Leader
>Abteilung fuer Evolutionsgenetik
>Institut fuer Genetik
>Universitaet Koeln
>Zuelpicher Strasse 47
>50674 Koeln - Germany
>new!!!: Tel: ++49 221 470 2324
>Fax: ++49 221 470 5975
>
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu