[BioC] VSN 2.2

[Hans-Ulrich Klein]

Dear all,

I want to normalize a matrix of gene expression values G using VSN. With 
VSN 1.x I did

 > vsnRes <- vsn(G)
 > Gvsn_old <- exprs(vsnRes) / log(2)

This still works with vsn 2.2 (besides deprecated warnings) and computes 
exactly the same values as the older version of vsn does. Now, with vsn 
2.2 I type

 > vsnFit <- vsn2(G)
 > Gvsn_new <- predict(vsnFit, G)

In both cases the normalization works. However, I noticed that the 
values are slightly different. It is not worth worrying about it, but  I 
would appreciate if someone could explain me the reason for that - just 
to satisfy my curiosity.

 > Gvsn_new[1:5,1:3] - Gvsn_old[1:5,1:3]
           01N         01T          03N
[1,] 0.1387763 -0.15328649 -0.011482728
[2,] 0.1398214 -0.09982814 -0.005172216
[3,] 0.1394453 -0.04704412  0.128297523
[4,] 0.1389546 -0.08527670  0.088480265
[5,] 0.1396382 -0.03739234  0.144517027


Regards,
Hans-Ulrich