[BioC] Problematic circular design

[Naomi Altman]

The simplest way to handle this in limma is to use a single channel 
analysis, using block=array.  The method is described clearly in the 
vignette.  MAANOVA will also handle this, although it might be a bit 
harder to set up.

There are several papers showing that in theory this is the most 
efficient design for 3 conditions with 2 channel arrays.  There are 
also several papers that confirm this experimentally.  The design is 
called a loop design.  For 3 conditions, the loop design is a 
balanced incomplete block design.

--Naomi

At 02:56 PM 9/6/2007, James W. MacDonald wrote:
>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
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111