[BioC] Limma contrasts questions
Sean Davis
sdavis2 at mail.nih.gov
Tue May 30 19:17:09 CEST 2006
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
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