DESeq2 to compare between samples

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2.9 years ago

wmsalsah • 0

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?

DESeq2 • 768 views

ADD COMMENT • link updated 2.9 years ago by andres.firrincieli 3.8k • written 2.9 years ago by wmsalsah • 0

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From the vignette :

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

ADD REPLY • link 2.9 years ago by Aspire ▴ 370

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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

ADD REPLY • link 2.9 years ago by andres.firrincieli 3.8k

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