Hello,
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:
1 answer
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Batch, subject, gender, drug, these are all just titles. DESeq2 does not know about it's meaning. If batch and subject have the same factorial values then the correction is the same, else it is different. Please show colData for a precise answer.
Thank you for your reply. I updated my question to make things a bit more clear.