[BioC] Is a set of four arrays suitable for RMA analysis?

[Wei, Wenbin]

Hello, 

 

I have a set of four Affymetrix HG-Focus arrays (including two controls and
two treatments) to be analyzed. I would like to know whether a set of four
arrays is suitable for RMA analysis.  In Irizarry et al.
(http://www.biostat.jhsph.edu/~ririzarr/papers/affy1.pdf
<http://www.biostat.jhsph.edu/~ririzarr/papers/affy1.pdf> ), the minimum
number of arrays in a set subjected to RMA analysis was five. 

 

In dChip manual, it is mentioned that "For better model fitting and outlier
detection, the number of arrays in a dChip group is desired to be more than
5. " (http://biosun1.harvard.edu/complab/dchip/prepare%20data.htm
<http://biosun1.harvard.edu/complab/dchip/prepare%20data.htm> ). 

 

Has anybody compared various methods available in the Affy package for the
analysis of a set of four arrays? Which is the best?

 

Wenbin Wei

Division of Cancer Studies

Birmingham University

Birmingham, B15 2TT

UK


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