Hi there,

Can I please ask a question

I get very different results when I perform Deseq2 by choosing 3 factor levels under 1 FACTOR vs performing Deseq2 individually 3 times to compare the three factor levels to each other So, I am unable to say which is the correct result.

DeSeq2 Run1 FACTOR 1: TREATMENT Factorlevel1: conditionA Factorlevel 2:conditionB Factorlevel 3: conditionC (I also checked the box that says :Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)

This one generates 3 result files comaring A vs B, B vs C and A vs C. However, these results are very different to that obtained when I run DeSeq2 individually as follows.

DeSeq2Run2 FACTOR 1: TREATMENT Factorlevel1: conditionA Factorlevel 2:conditionB

DeSeq2Run3 FACTOR 1: TREATMENT Factorlevel1: conditionA Factorlevel 2:conditionC

DeSeq2Run4 FACTOR 1: TREATMENT Factorlevel1: conditionB Factorlevel 2:conditionC

Can someone please help.

Many thanks, GG

This is a FAQ in the DESeq2 vignette.