[BioC] Rosetta vs Limma

[Nataliya Yeremenko]

Hello
I have a questions about correlation of outcomes from Rosetta and Limma.
I have done Agilent direct hyb's (one condition versus another).
In Rosetta I have splitted ratios without common references and than 
have done two sample Ttest.
In Limma I also splitted channels and than fitted linear model. I have 
posted design in previous BioC thread with subj "Design question in LIMMA".
The outcome of the Toptable is different (from 120 signatures only 20 
intersects).
Does anybody experienced that problem or have expertise of statistical 
treatment of twocolors direct ratio based arrays
in Rosetta and Limma simultaneously.

Regards,
Nataliya



-- 
Dr. Nataliya Yeremenko 

Universiteit van Amsterdam
Faculty of Science
IBED/AMB (Aquatische Microbiologie)
Nieuwe Achtergracht 127
NL-1018WS Amsterdam
the Netherlands

tel. + 31 20 5257089
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