[BioC] Affy analysis

[Yuk Fai Leung]

Hi,
 
I am going to do affy analysis for the first time. After reading the
previous related postings, I have some questions:
 
1. If I use the RMA method to estimate the true intensities, should I
neglect the present call/absent calls? 
2. If I should neglect the present/absent calls, is there any other another
equivalent variable that is similar to the weights or flagged poor values in
2-channel data?
3. If I should still use present/absent calls, are they included in the
latest affy package? How should I use the calls with the results generated
from RMA method? 
4. Any pointers, especially using affycomp, for choosing a good combination
of background correction, pmcorrection, normalization & summarization
methods? 
 
Thanks in advance!
 
Regards,
Fai
________
Yuk Fai Leung
Bauer Center for Genomics Research
Harvard University
7 Divinity Avenue
Cambridge, MA 02138
Tel: 617-496-7134
Fax: 617-495-2196
email:  <mailto:yfleung at cgr.harvard.edu> yfleung at cgr.harvard.edu;
<mailto:yfleung at genomicshome.com> yfleung at genomicshome.com
URL:  <http://genomicshome.com> http://genomicshome.com
 
 

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