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 














Looks good to me. From the dds table, you will just need to extract the contrasts now (VD vs wt and AT vs WT) using the `results()` function documented [here][1].


  [1]: https://rdrr.io/bioc/DESeq2/man/results.html