Can the DESeq2 object for paired data be set with design= ~ batch + condition?

Question

[bioinfo]

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:

[ATpoint]

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.

[bioinfo]

Thank you for your reply. I updated my question to make things a bit more clear.

Answer 1

[bk11]

Do you see any batch effect in your samples? If so, design= ~ batch + condition seems logical to me. Why would you have design= ~ subject+ condition? But if you think each sample is the batch then you could run `DESeq2 with second design.

[bioinfo]

I have updated my question to make things a bit more clear. I do not have batches in my samples. They were all run the same time but I have paired samples.

[bk11]

Then design= ~ batch + condition will be a good design for your experiment.

[bioinfo]

Thank you. I was wondering if it matters if the design is set up lie this: design= ~ batch + condition if on the sample table the first column is the condition and the second is the batch.

[bk11]

It should not matter with the column switch as far as I know.

[bioinfo]

Thank you so much!