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

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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.