[BioC] Limma factorial experiment: interaction parameter
donald.dunbar at ed.ac.uk
Wed Mar 30 11:52:49 CEST 2011
Thanks for that Oscar, it's a big help.
With best wishes,
On 03/29/2011 05:07 PM, Oscar Rueda wrote:
> Dear Donald,
> Yes, the contrast to test the interaction effect should be DH-DC-CH+CC
> If you don't get significant probes it means that the effect of the
> combination of the two drugs is the sum of the marginal effects; that
> could make sense depending on the nature of your experiment.
> Hope it helps,
> On 29/3/11 16:27, "Donald Dunbar" <donald.dunbar at ed.ac.uk> wrote:
> I have a gene expression experiment with four replicates each for four
> groups: control, two drugs and their combination.
> Control (C.C)
> Drug1 (D.C)
> Drug2 (C.H)
> Drug1+Drug2 (D.H)
> I have imported the Affymetrix data, normalised and set up a design to
> analyse in Limma.
> C.C D.C C.H D.H
> 1 1 0 0 0
> 2 1 0 0 0
> 3 1 0 0 0
> 4 1 0 0 0
> 5 0 1 0 0
> 6 0 1 0 0
> 7 0 1 0 0
> 8 0 1 0 0
> 9 0 0 1 0
> 10 0 0 1 0
> 11 0 0 1 0
> 12 0 0 1 0
> 13 0 0 0 1
> 14 0 0 0 1
> 15 0 0 0 1
> 16 0 0 0 1
> I initially set up contrasts and following lmFit, contrasts.fit,
> and decideTests find differentially expressed probe-sets:
> drug 1 v control contrast 'D.C-C.C' gives 46 probesets
> drug 2 v control contrast 'C.H-C.C' gives 233 probesets
> drug 1 + drug 2 combination contrast 'D.H-C.C' gives 3897 probesets
> Clearly there are several thousand probe-sets differentially expressed
> by the drug combination and not by the individual drugs. I can find
> these crudely by filtering the p-values of the contrasts, but I would
> rather do it properly.
> I would like to define an interaction parameter and select
> differentially expressed genes. I read Gordon Smyth's Limma user guide
> and several helpful posts on this list but have so far failed to
> find an
> appropriate parametrization. The user guide's factorial example has
> sepatare controls for each treatment group so isn't applicable for
> me I
> think. James MacDonald gave a helpful reply to Suzanne Szak in May
> and I thought I'd try that:
> (combo-control)-(x-control)-(y-control) but I think I'm
> his answer: if I try this (D.H-C.C)-(D.C-C.C)-(C.H-C.C) I get no
> significant probe-sets.
> My own idea was (D.H-D.C)-(C.H-C.C) but that also gave no significant
> probe-sets and I think was a bit silly.
> Any help on this would be greatly appreciated.
> With best wishes,
> Donald Dunbar
> University of Edinburgh
> donald.dunbar at ed.ac.uk
> Oscar M. Rueda, PhD.
> Postdoctoral Research Fellow, Breast Cancer Functional Genomics.
> Cancer Research UK Cambridge Research Institute.
> Li Ka Shing Centre, Robinson Way.
> Cambridge CB2 0RE
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donald.dunbar at ed.ac.uk
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