Help me In deseq2 design
I have factors sex, 2species, 5stages
I want to know differential expressed genes between male and female of one species and And then from this extract I want to compare male of this species to 2nd species male
In short Regress out female effect from each stage and other species male
I designed like
Design = ~ Replicate + sex + stage + species And made ref = female
And plan to use contrast
I think something is wrong Please help how could I do this in one design I able to extract above objective for all stages
Thanks in advance
gc have both sexes while tc have only male how to design this deseq2
dds <- DESeqDataSetFromMatrix(countData = Counts, colData = metadata, design = ~ Species + Sex + Stage + Replicate)
i am interested in two things DEG between male and female of Gc DEG between male of Gc and TC (for each stage as well as all combine for both comparisons)