[BioC] SAM q-values

[E Motakis, Mathematics]

Dear all,

I perfomred SAM analysis in my dataset and the sam.plot command that gave 
me estimates of the q-values for the significant genes. However all of 
those q-values were around 0.6.

Does anyone know how these q-values are calculated?

If the q-value is similar to p-value in interpretation, why these genes are 
significant?

Should I take into account the q-values estimates for my analysis? What can 
I say?

Thank in advance.
Makis Motakis

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