[BioC] How to pool subgroups for makeContrasts() and subsequent limma analysis?

[René]

> > Hi René,
> >
> >
> > You are almost there. Note that you want the mean of the three groups, 
> > not the sum. So
> >
> > makeContrasts((B1 + B2 + B3)/3 - A)
> >
> > will e.g., do the comparison of B vs A.
> >
> > Best,
> >
> > Jim

Dear James,

I performed the pooled analysis as you suggested and compared the results to a 
pure B - A comparison (no subgroups specified). Interestingly, both analyses 
give different results (497 vs 15 genes with log2FC >= 1 and p < 0.05).
Could you explain this huge difference?

Best regards,
René