[BioC] VSN and Quantile

[Lev Soinov]

Dear List,
   
  I have a question about normalization and would be very grateful for any comments.
  In my experiment, 4 control samples appear to be quite different from 4 treated samples, log intensity distributions of typical control and treated samples are attached to this letter.
  Could you please comment on whether the quantile normalization is applicable here, as distributions look quite different?
  Would it be more appropriate to use VSN here? As far as I understand, VSN does not assume identical distributions for arrays, but then, may be some other VSN assumptions may be violated here.
  I have thought about filtering out probes that are "unexpressed" across all samples and then quantile normalize (this would make distributions closer to each other), but I am not sure whether this is a good idea as many people prefer to normalize using ALL data.
   
  With kind regards,
  Lev.


       
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