Issue with DESeq: when using DESeqDataSet object what to put under argument design when there are 3 variables

Question

[catglen012]

Hello!

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.

Answer 1

[catglen012]

Would this be a solution to this:

dds$group <- factor(paste0(dds$celltype, dds$condition))
design(dds) <- ~ group
dds <- DESeq(dds)
resultsNames(dds)
# e.g. for condition KO cell type 2 vs cell type 1
results(dds, contrast=c("group","2KO","1KO")) 
# e.g. for cell type 1 KO vs WT
results(dds, contrast=c("group","1KO","1WT"))

except instead of 2 variables it is 3? Example:

dds$group <- factor(paste0(dds$celltype, dds$condition, dds$place))