I have one type of plant collected from 3 different localities (called population), and they are also 2 different sexes, and are at 2 different life stages (called stages).
My ultimate goal is for each locality, see how males and females are differentially expressed during each separate life stage.
Example: In Chicago (locality), how is my plant at the protonema stage, differentially expressed in males compared to females?
When I construct my object dds, I was wondering how can I make my dataset include only 1 locality but also include Sex, and life stages?
I am using the following so far:
dds <- DESeqDataSetFromMatrix(countData = countData, colData = colData, design = ~ Sex + Stage + Locality)
I have 3 replicates for each different locality, as well for each different sex, and life stage.
This is how the some of the first lines in my ColData look like:
gene_id, Stage, Sex, Population Chi_10.5_B150f_Gam_1,Gametophore,Female,Chicago Chi_10.5_B150f_Gam_2,Gametophore,Female,Chicago