[BioC] data transformation

[Wolfgang Huber]

Hi Rohit,

the results of vsn are invariant under scaling, i.e. the
result of

   vsn(x)

is the same as that of

   vsn(1000*x)

except for an overall additive offset of the transformed values by a 
value of log(1000).

Since log-ratios (strictly speaking, "generalized log-ratios") are 
differences between transformed values, it makes no difference between 
the two calls.

Hope this helps,
  Wolfgang


Rohit Ghai wrote:
> hello all
> I am trying to perform VSN normalization with one-color Codelink chip data.
> after normalization in vsn i start getting negative values all over the 
> expression
> matrix... this makes it difficult to get fold changes for the genes. how 
> can i get
> around this problem ? I think its because the raw intensity values i get 
> from codelink
> are a bit low. I also multiplied the raw data matrix by a factor of 2. 
> With the trasnformed
> data matrix VSN did not give any negative values, but the boxplots 
> looked a little upward shifted
> as compared to the non-trasnformed data. The final gene list that I got 
> (genes with a standard
> deviation of more than 2 in any experiment) was the same both with the 
> raw data and with the
> transformed data.. but I want to know if its alright to do this?
> any ideas would be appreciated
> 
> Rohit
> 
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-- 
-------------------------------------
Wolfgang Huber
Division of Molecular Genome Analysis
German Cancer Research Center
Heidelberg, Germany
Phone: +49 6221 424709
Fax:   +49 6221 42524709
Http:  www.dkfz.de/abt0840/whuber