Hi all,
I know that this is a frequently asked question, but I still haven't quite grasped how to build the formula design for a multifactorial paired study. My sample table is as follows:
Has.disease PatientName Replicate Treatment Individual
N Control 1 Ctrl 1
N Control 1 Epi 1
N Control 2 Ctrl 2
N Control 2 Epi 2
N Control 3 Ctrl 3
N Control 3 Epi 3
Y Patient1 1 Ctrl 1
Y Patient1 1 Epi 1
Y Patient1 2 Ctrl 2
Y Patient1 2 Epi 2
Y Patient2 1 Ctrl 1
Y Patient2 1 Epi 1
Y Patient2 2 Ctrl 2
Y Patient2 2 Epi 2
Y Patient2 3 Ctrl 3
Y Patient2 3 Epi 3
I'm interested in identifying those genes which have a different expression profile between disease/not-disease patients after treatment with Epi. I finally settled on a design formula of: ~Has.disease + Has.disease:Replicate + Has.disease:Treatment (per the vignette), but I really don't know 1) What exactly the formula is measuring, and 2) How I should set my corresponding contrasts.
As an aside, I've had a very hard time understanding when I should be using the : or the * interaction term in the design formula - I've had no luck with the DESeq2 documentation or on the online forums with finding a good guideline.
I know that this is a frequently asked question, but I still haven't quite grasped how to build the formula design for a multifactorial paired study. My sample table is as follows:
Has.disease PatientName Replicate Treatment Individual
N Control 1 Ctrl 1
N Control 1 Epi 1
N Control 2 Ctrl 2
N Control 2 Epi 2
N Control 3 Ctrl 3
N Control 3 Epi 3
Y Patient1 1 Ctrl 1
Y Patient1 1 Epi 1
Y Patient1 2 Ctrl 2
Y Patient1 2 Epi 2
Y Patient2 1 Ctrl 1
Y Patient2 1 Epi 1
Y Patient2 2 Ctrl 2
Y Patient2 2 Epi 2
Y Patient2 3 Ctrl 3
Y Patient2 3 Epi 3
I'm interested in identifying those genes which have a different expression profile between disease/not-disease patients after treatment with Epi. I finally settled on a design formula of: ~Has.disease + Has.disease:Replicate + Has.disease:Treatment (per the vignette), but I really don't know 1) What exactly the formula is measuring, and 2) How I should set my corresponding contrasts.
As an aside, I've had a very hard time understanding when I should be using the : or the * interaction term in the design formula - I've had no luck with the DESeq2 documentation or on the online forums with finding a good guideline.
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