DEseq2 with 3 factor levels only output one contrast group

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1

Hi -

I’m trying to use DEseq2 to compare three factor levels (a, b, c), where c is the control. When I run the program, I only get one result file, and the plots only shows the MA plot for b vs c.

Is there any way to designate contrast (eg. a-c, b-c), like in limma? Is there a reason that DEseq2 only shows b vs c? Thanks

2

Hi @billy.l
Try Output options > Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)
Hope this helps.
Kind regards,
Igor