Hi, if I wanted to use this design in order to take in account the batch effects:

dds = DESeqDataSetFromMatrix(countData = countData, colData = colData, design = ~ condition + batch)

Is it correct to use this colData?

               condition       batch

test1        test                1

test2        test                1

test3        test                2

control1   control           1

control2   control           1

control3   control           2

Or this colData?

               condition       batch

test1        test                A

test2        test                A

test3        test                B

control1   control           A

control2   control           A

control3   control           B

Thank you.

Riccardo

We recommend in our vignette to put condition at the end of the design formula. This is in case you forget and ask for results(dds), you would get the batch results, which is not what you want.

As long as batch is a factor, it doesn't matter how you label them.

It's safer to use letters, so you can't accidentally forget to make it a factor. (It wouldn't matter with just two batches, but if you had a numeric batch variables and > 2 batches it would be a serious modeling mistake.)