[BioC] Limma contrasts questions

[Sean Davis]

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.

Thanks,
Sean