I am trying to do deseq2 analysis but I have samples which were library prepped at different intervals. I have 3 wild type samples, 3 MUT samples and 3 drug treated samples

WT1 - 12/14/2022
WT2 - 12/14/2022
WT3 - 11/03/2021
MUT1 - 11/03/2021
MUT2 - 11/03/2021
MUT3 - 11/03/2021
DRUG1 - 11/03/2021
DRUG2 - 12/03/2021
DRUG3 - 11/03/2021

How can I make my sample info so as to include the batch column. Right now this is how my sample info looks like:

Sample  condition
mut_rep1    mut
mut_rep2    mut
mut_rep3    mut
drug_rep1   drug
drug_rep2   drug
drug_rep3   drug
WT_rep1        WT
WT_rep2        WT
WT_rep3        WT

Thanks

You just add another column. Use I, II and III if you don't want to deal with date format.

But I am not sure it's going to work. Every 12/14 is wild type. Your only 12/03 is Drug. I don't think you are going to be able to correct for batch effects, I think you are going to have to live with them. Make sure the people doing the experiment understand for next time that they have to do all the library preps for all samples on the same day.