Closed:Global test with custom gene sets and multiple samples

Question

[SB]

Dear Biostars,

I'm interested in using gt {globaltest} to perform gene set testing with two custom gene sets and three different sample groups (each with several replicates); however, I've been unable to set up the input variables to the gt function properly. I have started to set up the inputs as follows and would appreciate any feedback you could offer. Specifically, I'm unsure of what to provide (if anything) to "null", "data", "test.value", and "levels" as input.

Thanks,

SB

######## eset: a gene by sample matrix of expression values 
colnames(eset) <- rep(c("Group1","Group2","Group3","Group4"),each=3) 

f <- factor(colnames(eset),levels=unique(colnames(eset))) 

design <-  model.matrix(~0+f) # design matrix

colnames(design) <- unique(colnames(eset))

gene.sets = list(Set1=paste(S1), Set2=paste(S2))

gt(response=f, alternative=t(eset), null, data, test.value, levels,
   model = "multinomial", subsets=gene.sets,
   directional = FALSE, standardize = FALSE, permutations = 0,
   alias, x = FALSE, trace=TRUE)