Hello,

If I have two conditions, which were sequenced as two different runs, is there a way to normalize the data before running DESeq2?

For example: I have 8 samples 4 each of one condition age1, batch1 age1, batch1 age1, batch1 age1, batch1 age2, batch2 age2, batch2 age2, batch2 age2, batch2 Is there a way to normalize the impact of batch on these samples, before I do a differential expression analysis?

There is no way to separate the effect of batch from condition when they are completely confounded.