[BioC] limma design

[James W. MacDonald]

Lev Soinov wrote:
> Dear Gordon and List,
> 
> I would very much appreciate your comment on the experiment design in
> LIMMA. It is about processing of experiments with multiple
> treatments.
> 
> Let's say we have a simple Affy experiment with 16 samples collected
> from a cell line (treated/untreated) in two time points: - 4 treated,
> 4 untreated - time point 1 - 4 treated, 4 untreated - time point 2 We
> are interested in differential expression between treated and
> untreated cells, in point1 and point2 separately. When we process all
> samples together (normalise them together and fit linear fit models
> using the whole dataset) in LIMMA we will get results different from
> when we process data for points 1 and 2 separately (normalise them
> together but fit liner models separately).
> 
> I do understand that it should be like this (more information for
> priors), but I do not know whether there is some kind of a criterion
> helping decide whether to process them separately or in one go. It
> seems that adding more treatments into the mix increases statistical
> power and thus, increases the number of genes classified as
> differentially expressed. The latter seems a bit strange to me,
> because the number of genes classified as differentially expressed in
> one comparison (contrast) should not depend on the genes
> differentially expressed in some other comparison (contrast).

Yes, but you are fitting a linear model and then computing contrasts in 
one instance, and fitting two independent t-tests in the other. In the 
former, your denominator will be based on the SSR from the linear model 
(which is computed using data from _all_ samples, not just those being 
compared). In the latter the denominator is based on just those samples 
under consideration.

Best,

Jim



-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.