[BioC] VSN 2.2

Wolfgang Huber huber at ebi.ac.uk
Wed May 2 20:57:11 CEST 2007

Dear Hans-Ulrich,

the function "vsn" has not changed, it is identical to previous 
releases. If there is demand, I can leave it there for quite a while.

"vsn2" optimizes the same likelihood function, but the implementation is 
different (and I hope better). There will be numerical differences, but 
they should not be consequential. If someone does discover substantial 
differences, please tell me, this should in general not happen. However:

1. I did change the way the overall baseline (additive offset) of the 
result is computed (see "Value" section of vsn2 man page), before, that 
was based on array number 1, now it is based on a mean of all arrays.

2. The likelihood function can sometimes be quite flat, and the maximum 
found by numerical optimization can vary. In these cases, different 
normalization parameter values are almost as good as each other, i.e. 
the result may numerically differ but not in a consequential manner.

3. In some (ill-determined) cases, the optimizer may run off into outer 
space and converge in a meaningless local maximum... Some quality 
control and sanity check on the result (function "meanSdPlot") is always 

Hope this helps, please let me know,

How do the scatterplots of old versus new glog-ratios look like?

  Best wishes

  Klein wrote:
> 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
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Best wishes

Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber

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