[BioC] dif between toptable and topTable

[Sebastien Gerega]

Hi,
I can see in the topTable documentation that "|toptable| is an earlier 
interface and is
retained only for backward compatibility." However, if this is the case 
I would have
thought I would get the same results with both methods. Instead this is 
what I get
with topTable
               ID p.s.X.n.s.X        t        F      P.Value    adj.P.Val
10878 201429_s_at -0.10536776 14.17887 42456.21 5.325611e-29 9.481334e-26
18250 208834_x_at -0.01423163 14.00786 41650.35 6.079627e-29 9.481334e-26
22094 212788_x_at  0.01454676 14.20958 41614.89 6.115511e-29 9.481334e-26
18241 208825_x_at -0.02691777 14.00615 41546.70 6.185202e-29 9.481334e-26

and this is what I get using toptable
          logFC        t      P.Value    adj.P.Val        B
36960 13.278474 55.61688 1.183004e-17 6.468076e-13 28.81054
32762  9.208360 49.09926 6.570132e-17 1.284238e-12 27.66241
54191 10.949433 47.88478 9.270056e-17 1.284238e-12 27.41920
14250  7.630690 47.83800 9.395430e-17 1.284238e-12 27.40963

the p-values are different as are the columns provided.
Is this right, and if so why is it the case?
thanks,
Sebastien