[BioC] normalization for custom chip

[Wolfgang Huber]

M Inmaculada Barrasa wrote:
> Hi Wolfram,
> I read this in a previous e-mail on this thread.
> 
>> I do not recommend using house keeping genes for normalization. In
>> several experiments they turn out being differentially expressed.
 >> A better approach would be to use a normalization method that searches
 >> for an invariant set of genes in the sample. "VSN" and Li & Wong's
 >> "invariant set" do that. The methods have limits though regarding
>> the minimum proportion of not differentially expressed genes.
 >> Below 30% things become difficult. ....
> 
> 
> Can you please give more details on how would you apply  VSN to search for
> invariant set of genes that can be later used to normalize the array.
> 
> Sorry if I am making so sense.
> I will read your paper carefully
> 
> Inma

Hi Inma,

vsn does not directly search for an "invariant set". Rather, it regards 
the fitting of scale factors and background offsets as a parameter 
estimation problem and uses a standard robust estimation technique for 
this. The performance of this estimator, and in particular the 
sensitivity to total number and asymmetric proportions of up- and 
down-regulated genes, is discussed in (hopefully exhaustive) detail in 
the paper

Parameter estimation for the calibration and variance stabilization of 
microarray data. W. Huber, A. von Heydebreck, H. Sültmann, A. Poustka, 
M. Vingron. Statistical Applications in Genetics and Molecular Biology 
2003 Vol. 2: No. 1, Article 3
http://www.bepress.com/sagmb/vol2/iss1/art3

in particular, Fig. 8 shows that up to about 30% of differentially 
expressed genes are OK that are all up or all down, and more, if they 
are more symmetric.

-- 
Best wishes
   Wolfgang

-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Http:  www.dkfz.de/abt0840/whuber