Hi

I have 5 groups and 3 levels of batches. This is my code:

rna.o=DESeqDataSetFromMatrix(data,colD,design = ~projects+Subtypes)

rna.d.pair=DESeq(rna.o,parallel = T)

this is my resultsNames:

resultsNames(rna.d.pair) [1] "Intercept" "projectsPACA.CAvsPACA.AU" "projectsPAEN.AUvsPACA.AU" [4] "Subtypes2vs1" "Subtypes3vs1" "Subtypes4vs1"
[7] "Subtypes5vs1"

For the next step, how should I use contrasts for one vs multiple groups for example 2 VS 1,3,4,5?

If you use a design of ~0 + condition + batch, then you will have a coefficient for each level of condition. This is one of the cases where it helps to not have condition at the end of the design (for convenience, we often recommend to put condition at the end, but not in this case).

Then you can do:

results(dds, 
        contrast=list(c("conditionA"), 
                      c("conditionB","conditionC","conditionD","conditionE")),
        listValues=c(1, -1/4))

if you wanted to compare A to the average of B-E.