[BioC] LIMMA: analysis of direct design....

[Gordon Smyth]

This is an example of a "three group" problem. See the section called 
"Several Groups" in the limma User's Guide, version 1.8.18 or later. You'll 
find this in the Bioc developmental repository or at 
http://bioinf.wehi.edu.au/limma

You want the "group-means" parametrization for the design matrix, which 
tells you which genes are DE for each method, and pairwise differences 
contrasts, which tells you how different the methods are.

Gordon

>Date: Tue, 8 Feb 2005 17:05:28 +0100
>From: "Jakob Hedegaard" <Jakob.Hedegaard at agrsci.dk>
>Subject: [BioC] LIMMA: analysis of direct design....
>To: <bioconductor at stat.math.ethz.ch>
>
>Hi!
>
>
>
>We have data from an experiment conducted to compare three different
>methods (1,2 and 3) for amplifying RNA. RNA from two tissues (A and B)
>were amplified with the three different methods and labeled. The same
>dye was assigned to the same tissue in all hybridizations (no dye-swap).
>Three slides were hybridized within each method.
>
>
>
>Slide     Method Cy3      Cy5
>
>1          1          A          B
>
>2          1          A          B
>
>3          1          A          B
>
>4          2          A          B
>
>5          2          A          B
>
>6          2          A          B
>
>7          3          A          B
>
>8          3          A          B
>
>9          3          A          B
>
>
>
>The data from each slide is background corrected and loess normalized
>within each slide followed by quantile normalization between slides.
>
>We want to test whether the three different methods reveal the same
>genes to be differentially expressed between tissue A and B - and
>whether two of the methods resemble each other more than the third.
>
>
>
>
>
>How should the design/contrast matrix look like?
>
>
>
>
>
>
>
>-------------------------------------------------------------------
>
>Jakob Hedegaard
>
>Danish Institute of Agricultural Sciences
>
>Department of Genetics and Biotechnology
>
>Molecular Genetics and System Biology
>
>Building K25
>
>Research Centre Foulum
>
>P.O. box 50
>
>DK-8830 Tjele
>
>Denmark
>
>Tel: (+45)89991363
>
>Fax: (+45)89991300