Deseq2 with continous variable

Question

[David]

Hi, I would to see if there us any gene differentially expressed based on a continous variable (temperature) over age. I want to know exactly if there any genes that differ over age.

I have the following design:

design(dds) = ~ Agegroup:temperature

Agegroup has two factors: 20_40 and 41_70

DESeq(dds)

I obtain the following results:

resultNames(dds) [1] "Intercept"
"AgeGroup_20_40.temperature" "AgeGroup_41_70.temperature"

To get those genes i run:

results(dds,name="AgeGroup_20.40.temperature")

Do i understand correclty this is returning only differentially expressed genes within the group 20_40 ? How do i get those differentially expressed between the two age groups at different temperatures ?

Answer 1

[Kevin Blighe]

You need to re-order the levels of your Agegroup variable. In your example, AgeGroup_20.40.temperature is being compared to AgeGroup_41_70.temperature. Perhaps this is already what you want.

Kevin