I have a problem in incorporating the output of sva into limma analysis. Specifically it is my newness to matrix design thats causing the problem.
I'd like to do a simple DE analysis between two states: DIS and TE. The surrogate variables (4 of them found by sva can be seen here in my modSv file:
> modSv (Intercept) DIS TE 1 1 0 0 0.170511776 -0.026039142 0.1551621788 2 1 0 0 -0.031146292 0.231081859 -0.1192856157 3 1 0 0 0.304738317 -0.114059097 0.0561335693 ... 1 -0.052378086 2 0.020441932 3 -0.008361104 ...
Now the sva manual gives an example of how to incorporate modSv into the process of making a contrast matrix, but I am not sure if their example:
> contrast.matrix <- cbind("C1"=c(-1,1,0,rep(0,svobj$n.sv)),"C2"=c(0,-1,1,rep(0,svobj$n.sv) > fitContrasts = contrasts.fit(fit,contrast.matrix)
Is designing the same sort of matrix I would need. In this matrix of theirs the surrogate variables are not being used in the contrast, as they are just used to adjust the analysis, the "rep(0,svobj$n.sv)" is basically just saying "place the same number of 0s as their are surrogate variables as recorded in the file svobj.
My question is this: What would be the appropriate way of designing a matrix for my comparison of DIS to TE ignoring surrogate variables? Would it actually be very similar to their example?
I'd appreciate any help you can offer!