How to perform DESeq2 based on paired sample test?

Question

[wmsalsah]

I'm using DESeq2 to do differentially expression analysis. My samples include patients before and after treatment without replicate, as well as cell lines before and after treatment with replicate. Two of my treated cell lines are Drug tolerance persister (DTP) cell and Drug tolerance proliferating persister (DTPP) cell.

My goal is to run DESeq2 on a paired sample test. So here are my questions:

1. Is it OK to use the paired sample test in patients even if there is no replicate?

2. Can I consider the cell lines treated with DMSO before treatment (control) and use it for paired sample test?

3. Is it acceptable to perform the paired sample test for DTP and DTTP cell lines with the control (not DTP or DTTP), or should I eliminate cell lines containing DTP and DTTP?

Answer 1

[Vitor1]

I would take a look at

How to run the Deseq2 tool without replicates.

https://support.bioconductor.org/p/101210/

And a variety of other posts with the same topic.

1. So no, its not ok to use deseq2 or even edger with no replicates.
2. Yes, you can use the cells treated with DMSO (the same final concentration as if wast treated with the drug, If it was in what the drug was dilluted in) as controls for the treated cells, not for the patients.
3. Didnt quite get the question, but you can compare the DTP with DMSO, and also DTTP with DMSO, since they are independent samples, independently of the counts beign in the same table.