Hi all,

I am analyzing single color data from Agilent using limma. The experimental
design include a common reference (4 biological replicate), after 1hr
treatment( 4 biological replicates) and after 3 hour treatment (4 biological
replicates). The adjusted P values are higher than 5% FDR in all the three
types of analysis (reference vs Ihr treatment, reference vs 3hr treatment
and 1hr treatment vs 3hr treatment)

I this scenario I would like to do gene filtering, but what should be the
pipeline for filtering? whether I should perform filtering in raw data or
after normalization. And I am just wondering whether I could get a better
FDR values without losing biologically important genes even after filtering?

Appreciate the guidanc ein advance.



-- 

Regards,
Abhilash

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