[BioC] Differential expression

[E Motakis, Mathematics]

Dear all,

I am working on two colours microarray experiments and, from a set of 42000 
genes, I would like to identify the differentially expressed ones. I have 
read several articles on this issue and most of them imply that the number 
of differential expressed genes in such experiments should be a small 
number (compared to the whole set).

Could anyone tell me why this is correct? What if I find half of the genes 
to be differentially expressed according to the t-test p-value?

I am not discussing the issue of p-values and q-values yet. I am asking 
only about why most of the papers imply a low number of differentially 
expressed genes.

Thank you,
Makis


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E Motakis, Mathematics
E.Motakis at bristol.ac.uk