[BioC] Limma contrasts questions

[James W. MacDonald]

Hi Sean,

Sean Davis wrote:
> Just ANOTHER limma contrast matrix question:
> 
> I am trying to compute some contrasts of interest and have three factors:
> 
>  Treatment (Hypoxic,Norm)
>  Tissue (4 levels)
>  Genotype (WT,KO)
> 
> I chose a parameterization like this for the design matrix:
> 
> 
>>colnames(design)
> 
>  [1] "TSBrain.Hypoxic.KO"  "TSBrain.Hypoxic.WT"  "TSBrain.Norm.KO"
>  [4] "TSBrain.Norm.WT"     "TSHLM.Hypoxic.KO"    "TSHLM.Hypoxic.WT"
>  [7] "TSHLM.Norm.KO"       "TSHLM.Norm.WT"       "TSKidney.Hypoxic.KO"
> [10] "TSKidney.Hypoxic.WT" "TSKidney.Norm.KO"    "TSKidney.Norm.WT"
> [13] "TSLiver.Hypoxic.KO"  "TSLiver.Hypoxic.WT"  "TSLiver.Norm.KO"
> [16] "TSLiver.Norm.WT"
> 
> I would like to determine the effect of the KO as compared to the WT.  What
> might a contrast matrix look like?  How about Kidney versus liver?  And the
> effect of the KO as compared to WT in liver?  I have looked at the limma
> guide and thought I had the idea, but this is slightly more complicated than
> the limma example given.

Getting out the main effects with this design matrix will be a pain. If 
I am not mistaken, your contrasts matrix should look like this (colnames 
omitted for clarity - they are in the same order as you mention).

0.125	0	0
-0.125	0	0
0.125	0	0
-0.125	0	0
0.125	0	0
-0.125	0	0
0.125	0	0
-0.125	0	0
0.125	0.25	0
-0.125	0.25	0
0.125	0.25	0
-0.125	0.25	0
0.125	-0.25	0.5
-0.125	-0.25	-0.5
0.125	-0.25	0.5
-0.125	-0.25	-0.5

Remember that a contrast is simply adding/subtracting coefficients with 
the constraints that the coefficients on each side of the comparison sum 
to one, and overall sum to zero. Hence, in the first case we are adding 
and subtracting 1/8, the second 1/4, and the third 1/2.

Best,

Jim


> 
> Thanks,
> Sean
> 
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-- 
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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