[BioC] Problematic circular design

[James W. MacDonald]

Hi Daniel,
Daniel Brewer wrote:
> Hi,
> 
> I have just been handed a project that looks like the experimental
> design has not been ideal and I was wondering if anyone had any ideas
> how I could get something out of it.
> 
> Here is the design:
> 3 microarrays
> Array 1: A vs B
> Array 2: B vs C
> Array 3: C vs A
> 
> Where A, B, C are different samples.

Back when I was doing two color work, this was considered the height of 
good experimental design (the reference design was disparaged because 
you were wasting half of your time/effort on samples with no intrinsic 
value). Maybe things have changed?

Anyway, the maanova package will certainly handle this sort of analysis. 
A pubmed search for Kerr and Churchill will result in lots of hits for 
the papers they wrote describing the model they use to fit these data. 
The maanova package also has a vignett in which they analyze an 
experiment that is sort of similar.

I don't see why you couldn't use limma either. I don't know offhand what 
the design matrix would look like (as I mentioned, it's been years since 
I did two color stuff), but I am sure there is something in the limma 
User's Guide that you could use to figure things out.

Best,

Jim



> 
> The question that the experimenter would like to ask is what are the
> similarities between the three samples and what are the differences.
> Has anyone got any bright ideas how to proceed?  Without a control I
> can't really see how to do this.
> 
> Thanks
> 
> Dan


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