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!!!