Hi all, The main question is if someone has figured a way to automate the comparison of all possible combination? In more detail: I would like to continue on the problem of itteration all possible combinations among different conditions. (as seen in questions: comparisons morecomparisons and a few others) If the condition are more than 2 then the coef will only do conditions based on what is the first enry on the sampleTable for column "group": So it will do for A,B,C,D AvsB, AvsC and AvsD but NO BvsC or BvsD or CvsD. The initial function I can automate it as follows:

dds <- DESeqDataSetFromMatrix(countData = as.matrix(countTable),
                                colData = sampleTable,
                                design = ~ group)

I am using the following to run the lfcShrink() for all possible comparisons:

for (i in 2:length(resultsNames(dds))) {
    comparison <- strsplit(resultsNames(dds)[[i]], "_")
    res.raw <- lfcShrink(dds, type = "apeglm", coef = resultsNames(dds)[i])
    name <- paste0(as.data.frame(comparison)[2,1], "_",as.data.frame(comparison)[3,1],"_", as.data.frame(comparison)[4,1])
    res1 <- list(name = res.raw[order(res.raw$padj),])
    names(res1)<- name
    res <- append(res, res1)
}

In order to do the other comparisons, as BvsC I will need to do the following:

dds$group <- relevel(dds$group, ref = "C")  
dds <- nbinomWaldTest(dds)

and then

dds$group <- relevel(dds$group, ref = "D")  
dds <- nbinomWaldTest(dds)

But I can not really figure out how to

Question1: is there a "nice" way to automate this? Can I remove the main comparison factor ("A" in this case and redo the whole thing again) so that some comparisons will not redone?

I hope that the question is clear. Also, I already have implemented a for loop with ashr that produces a list (res as in the example above) with all given comparisons.

We don't have a way to automate all comparisons. What you've sketched out is how I would approach it. Easiest is to use ashr with pairwise combinations I would say.