Hi, I would be thankful for replies to my question related to gene set analysis with camera. Following is the problem:
Consider the example given on camera help page (?camera).
y <- matrix(rnorm(1000*6),1000,6) design <- cbind(Intercept=1,Group=c(0,0,0,1,1,1)) # First set of 20 genes are genuinely differentially expressed index1 <- 1:20 y[index1,4:6] <- y[index1,4:6]+1 # Second set of 20 genes are not DE index2 <- 21:40 camera(y, list(set1=index1,set2=index2), design)
The above example deals with comparison of two sample groups as one can see in the object, design.
I have more than two sample groups and I want to compare for example group 2 and group 3. So, the group = c(1,1,2,2,3,3).
How to build design matrix for such comparison and what to supply to "contrast" parameter?
Thanks in advance!