DESeq2 Design Matrix Two Conditions and Two Treatments


I kindly ask for help comparing the interactions terms between two groups. I have two groups (two conditions/types) and two treatments. the meta data is as follows

  sample              type treatment
1  Control_ND_1 Control        ND
2  Control_ND_2 Control        ND
3  Control_ND_3 Control        ND
4  Control_ND_4 Control        ND
5   Control_D_1 Control         D
6   Control_D_2 Control         D
7   Control_D_3 Control         D
8   Control_D_4 Control         D
9  Injured_ND_1 Injured        ND
10 Injured_ND_2 Injured        ND
11 Injured_ND_3 Injured        ND
12 Injured_ND_4 Injured        ND
13  Injured_D_1 Injured         D
14  Injured_D_2 Injured         D
15  Injured_D_3 Injured         D
16  Injured_D_4 Injured         D

D represents a special diet, and ND represents normal diet.

I want to compare the difference in gene expression between the Injured Group With Special Diet vs. Control Group with no diet (ND).

Running DESeq as follows:

dds$treatment = relevel( dds$treatment, “ND”) #Setting references

dds$type=relevel(dds$type,”Control”) #Setting references

design(dds)<- ~ type + treatment + type:treatment

res <- DESeq2(dds)

The result names of res are:





How would I use the results function to compare the Injured_D group vs. Control_ND group? I want to see the combined effect of having a special diet and being injured relative to the control group (injured) that has a normal diet. This is essentially comparing Samples #1-4 vs. Samples #13-16

Thank you so much!!!

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