[BioC] calibrating an exprSet on a specific probeset

Celine Carret ckc at sanger.ac.uk
Mon Oct 31 18:56:42 CET 2005


I'm sure what I want to do is really simple and straight forward, but 
right now I can't think of how doing it! I work on custom Affymetrix 
arrays, no MM features.
I have a filtered eset object pre-processed by RMA, quantiles 
normalisation and median polishing summarisation of the probesets. 
Because the question I'm asking to the experiment is very tedious, I 
want to make sure that all the probes matching the  5.8s rRNA are 
calibrated to the same level, even if the amount and quality of starting 
RNA is different.
I tried the affy.scalevalue.exprSet() function but it does scale the 
whole chips, regardless of the probesets I want to act as controls of 
the expression level.
Can someone please point me out on the right function ?

Thank you very much for your time and help,
(R2.2.0 & affy 1.8.1)

Celine Carret PhD
Pathogen Microarrays group
The Wellcome Trust Sanger Institute
Hinxton, Cambridge CB10 1SA, UK.
tel. +44 (0)1223 834 244 ext.7123
fax. +44 (0)1223 494 919
email: ckc at sanger.ac.uk

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