Dear Jose,
   
  I meant log trasformed raw data of course.
  Sorry for any misunderstanding. The plots that I posted were on the log2 scale.
   
  Thank you,
  Lev.

J.delasHeras@ed.ac.uk wrote:
  Quoting Lev Soinov :

>
[...]
> Also, it is often assumed that log transformed raw signal is 
> roughly Normal.

where do you get that idea?

My raw signals are anything but normally distributed! In fact, they 
look a lot like yours.
The *log ratios*, however...

And the distribution depends a lot on the actual array and the actual 
experiment. I was recently looking at some yeast tiling arrays probed 
with the product of doing chromatin immunoprecipitation with an 
antibody against a protein that is present along the body of genes. 
Almost everywhere, in fact, given the gene density of yeast. In this 
particular case, the raw data looks entirely different to yours (and 
to the arrays I usually deal with). The log ratios, however...

Jose

-- 
Dr. Jose I. de las Heras Email: J.delasHeras@ed.ac.uk
The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360
Swann Building, Mayfield Road
University of Edinburgh
Edinburgh EH9 3JR
UK

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