DESeq2 paired plus condition

[bioBob]

Hi,

I am having some trouble getting my head around it today, its Monday.

Essentially, I have a design matrix like so:

Patient Condition
58 2
58 3
64 2
64 3
...

So, according the the vignette, I need to do ~Patient + Condition. I really want condition differences, NOT patient differences.

I can view the results via results(slim_dds_1, contrast=c("Condition","3","2")). How do I know what was a patient difference? I suppose I could do the reduced formula and compare?

[dpryan]

You're going to need to provide rather more detail.

[fanli]

You can extract patient differences like so:

results(slim_dds_1, contrast=c("Patient", "58", "64")

Specifying the design as you did will explicitly account for differences in Patient when looking at Condition.

[dpryan]

@bioBob: for future reference, we don't get easily notified when a post gets edited. For a speedier reply, post a comment after editing (or just post the edit as a new comment). Anyway, I suspect that fanli answered your question. If instead you really want to see what genes vary with patient in general (i.e., not between any individual pair of patients but generally across them), then you can use the LRT test with a reduced model of ~Condition.