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!

Presuming you have already done differential expression analysis with limma or edgeR, your design matrix and contrasts for the camera are the same. I would suggest checking out limma user guide: http://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf

Since you can't use 1, 2 and 3 as group names, as they are not syntactically valid names in R, say your group labels are actually:

group = as.factor(c("a","a","b","b","c","c"))

Then your design matrix is:

des <- model.matrix(~0+group)
colnames(des) <- levels(group)

And the contrast to compare group c vs group b is:

contr <- makeContrasts(c-b, levels = des)

Hope it helps,

Aliaksei.

Thanks a lot Aliaksei! That helped!!