[BioC] Logged or unlogged data for multtest and limma?

[James W. MacDonald]

Ken Termiso wrote:
> Hi all,
> 
> As we all know, rma & gcrma return log2 values, while li-wong and mas5 
> results are unlogged. I'm pretty sure that limma wants logged data, but 
> how about multtest?

Although multtest uses a permuted null distribution and thus there is 
not necessarily an assumption of normally distributed (or at least 
roughly symmetrical) data, I think it is still prudent to log. This is 
because you are still using means, which are not robust to outliers.

> 
> Thanks in advance,
> Ken
> 
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-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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