[BioC] ChIP on Chip normalization

[Wolfgang Huber]

Hi Sean,

> In data we have looked at, the centrality paramater (whatever that is) 
> is often not correct, as chIPchip data is effectively one-sided.  This, 
> of course, depends on the experiment (high enrichment leads to a skewed 
> distribuiton of ratios). 

Agree. It might be worthwhile in this context to look at the "midpoint 
of the shorth" as a centrality parameter (function "shorth" in the 
genefilter package), it  is often less susceptible to asymetric tails 
than mean or median (see also the example in the man page).

The outlier detection in "vsn" tries to be quite robust against such 
asymmetric tails (and there is a simulation study in the paper cited 
below about this). I think loess also is robust against these to a 
certain extent, but not so sure how much.

[1] http://www.bepress.com/sagmb/vol2/iss1/art3/

Best regards
   Wolfgang

-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber