[BioC] vsn on log2 transformed data?

Wolfgang Huber huber at ebi.ac.uk
Sun Jun 4 21:12:04 CEST 2006

Kamila Naxerova wrote:
> Hi!
> Could anyone explain to me *why* I cannot apply vsn to log2 transformed 
> data? "...may not satisfy the requirements of the 
> multiplicative-additive noise model" is a little hard to grasp for 
> someone without a rigorous statistical background and the vignette and 
> the original publication did not enlighten me very much. Does this 
> really mean I cannot use vsn on a data set that contains log2 
> transformed ratios from a dual channel experiment?
> Thanks for any help!!!
> Kamila

Hi Kamila,

it is the same reason why you wouldn't apply the log transformation 
again on log transformed data, as James has already pointed out.

This question has come up before, and I've even seen this done in 
published papers: please, please, users, don't call vsn on 
log-transformed data or on log-ratios, it is non-sensical.

Note that for many practical purposes (if you don't care about maths), 
vsn is similar to

     x -> log( s*(x+x0) )

and what vsn has is a good way of estimating the parameters s and x0 
(which may be negative). Many other people call this simply "background 

If you look at two-color data, s and x0 are estimated separately for 
each channel, the data are transformed, then the difference is taken.

If you want to know what vsn does exactly, it is the transformation

    x -> log ( s/2*x + s/2*sqrt ( x^2 + x0^2 ) )

this results from the additive-multiplicative error model (which is 
arguably the most simple error model that fits to microarray data)

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

More information about the Bioconductor mailing list