[BioC] A question about MAS5 vs RMA vs GCRMA

[YUK FAI LEUNG]

Hi there,

I am helping my friend to do some analysis on his affy data. He has a 
simple 2x2 factorial experiment without any replication, i.e. only 4 
chips. Because of this, I just perform MAS5, RMA and GCRMA on the raw 
data with the default settings, and compute the fold changes of 
individual factor comparison. I am suprised to see that there are many 
more genes which have >= 2 fold change in MAS5 compare to the other two 
algorithms. For example in one comparison, MAS5 gives 21477 genes >= 2 
fold, while RMA gives 0 and GCRMA gives 4.

While I do know that RMA gives less significant genes, I do not expect 
to see such a drastic difference. Especially when his experiment is a 
drug treatment on a cell culture which is known to change a lot of 
genes, I am expecting to see a lot of changes even in the fold change 
comparison. Is this discrepancy occured due to the lack of replication?

Regards,
Fai
-- 
Yuk Fai Leung
Department of Molecular and Cellular Biology
Harvard University
BL 2079, 16 Divinity Avenue
Cambridge, MA 02138
Tel: 617-495-2599
Fax: 617-496-3321
email: yfleung at mcb.harvard.edu; yfleung at genomicshome.com
URL: http://genomicshome.com