[BioC] GCRMA/RMA bimodal distribution

[James W. MacDonald]

Matthew Hannah wrote:

> Hi,
> 
> Sorry for including the developers, but I guess you are the only ones
> that will be able to answer this, (and I'm not sure BioC accepts .docs).
> I saw a comment from Jean addressing the same question but couldn't find
> the reply he referred to. 
> 
> https://www.stat.math.ethz.ch/pipermail/bioconductor/2004-August/005769.
> html
> 
> It seems the mouse chip exprs values have a double peak after gcrma
> (looking at a density plot).

I don't understand the concern here for the distribution of expression 
values on a given chip (maybe I am missing something?). Is there 
something inherently wrong with a bimodal distribution, or are you 
simply assuming that the distribution of expression values on a chip  is 
supposed to be semi-normal (or at least unimodal)?

Note that any statistical test that I can think of (if we assume columns 
= samples and rows = genes) is done on a row by row basis, so I could 
see a concern if the row data were not all unimodal but what assumption 
applies to the columns?

Best,

Jim


-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109