I have 4 biological replicates of mRNA samples. For my dds, I am comparing type but have also added in the replicate factor to account for the biological replicates.
Is this correct? I have a column specifying the replicate number (1, 2, 3, or 4) per sample as they do not have the same names.
dds <- DESeqDataSetFromMatrix(
countData = counts_data,
colData = metadata,
design = ~ Replicate + Type # accounting for biological replicates
)