Question: Global test with custom gene sets and multiple samples
gravatar for SB
11 weeks ago by
SB0 wrote:

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.



######## 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)
globaltest gene set testing R • 155 views
ADD COMMENTlink modified 11 weeks ago by genomax65k • written 11 weeks ago by SB0
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