DESeq2 to compare between samples

Question

[wmsalsah]

I want to use DESeq2 to compare between samples before treatment and after treatment individually as paired samples. For example Pt.1 before vs Pt.1 after Pt.2 before vs Pt.2 after Pt.3 before vs Pt.3 after …

But I’m not sure if the DESeq2 compares patients individually (Pt.1 before vs Pt.1 after) or as a group (all patients before vs all patients after)?

and How to perform DESeq2 for paired samples for each patient individually, or is it acceptable to compare the groups (before vs after) rather than individuals?

[Aspire]

From the vignette :

http://www.bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#can-i-use-deseq2-to-analyze-paired-samples

[andres.firrincieli]

It seems like you do not have replicates (see previous post). So, the only think you can do is all patients before vs all patients after