I m using deseq2 for my samples such as Wild type[untreated] , and two treated condition [with vitamin D] and Retinoic acid 

and my samples are in replicates ,I want to compare the differential expression between WT vs treated[Vitamin D] and WT vs Retinoic acid .so here is my code im using but Im not sure if its doing what i want to do..

    condition <- factor(c(rep("WT", 2), rep("AT", 2),rep("VD",2))))`


    (coldata <- data.frame(row.names=colnames(countdata), condition))`
    dds <- DESeqDataSetFromMatrix(countData=countdata, colData=coldata, design=~condition)
    dds



Any suggestion or help would be highly appreciated 














Given your design, you'll want to ensure that `WT` is the base level for comparisons, which it's currently not.

    condition <- factor(c(rep("WT", 2), rep("AT", 2),rep("VD",2))), levels=c("WT", "AT", "VD"))

Now when you use `results()` the coefficients (2 will be AT vs. WT and 3 will be VD vs WT) will be the comparisons you want.