[BioC] question regarding unbalanced two way anova with interactionterm

[Kuhn, Max]

James,

The underlying issues is that the interaction model requires all 4 cells
to compute the interaction term. Essentially the interaction term is
defined as a contrast between the four cell means. Since one does not
exist, the interaction term is not estimable. 

Max


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of James
Anderson
Sent: Friday, August 17, 2007 6:12 PM
To: bioconductor
Subject: [BioC] question regarding unbalanced two way anova with
interactionterm

Hi,

I am having trouble understanding the following:

Suppose I have one gene with 26 samples. The first 20 samples are in
batch A, the remaining 6 samples are in batch B. In the first 20
samples, there are 12 samples in control group and 8 samples in treated
group, all batch B samples are in treated group.  When I use a linear
model (no interaction between batch and treatment), I can get some
values out of it. However, when I use model with interaction, the
variance are all 0, there must be something wrong with the model. I
understand this is not a good experimental design, however, I don't
understand why this kind of design will yield such kinds of results.
Could any one explain to me why? 

Thanks,

James

       
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