I was given the output of DESeq2 and the DESeq2 script for some paired data and I noticed that in the script the design was set as
design= ~ batch + condition instead of
design= ~ subject+ condition.
Is that considered the same thing or does DESeq2 perform a different correction when batch is set? I was wondering if I should rerun my data.
In my data S1-S3 are replicates of control and S4-S6 are replicates of treated. S1 is paired with S4, S2 with S5 and S3 with S6. Everything was prepared at the same time so I do not have batches. I was wondering if changing the batch to subject will change the results. The table would still be the same except for that.
Should i rerun it and change the batch to subject or is it the same thing?
The table was set like this: