Hello,
I am analyzing my experiment using DESeq2 I have 3 genotypes (1 Control + 2 mutants) and 3 treatments (1 Control + 2 treatments) and I have 4 technical replicates for each sample, I have done the count for the raw reads using HTSeq and I have the counts data, I need to get the differences between genotypes and treatments. which model should I use for my experiment?
Thank you
this is how the sample file look like:
sampleID cultivar treatment
g1-1 g1 Control
g1-2 g1 Control
g1-3 g1 Control
g1-4 g1 Control
g1-1 g1 Treat1
g1-2 g1 Treat1
g1-3 g1 Treat1
g1-4 g1 Treat1
g1-1 g1 Treat2
g1-2 g1 Treat2
g1-3 g1 Treat2
g1-4 g1 Treat2
g2-1 g2 Control
g2-2 g2 Control
g2-3 g2 Control
g2-4 g2 Control
g2-1 g2 Treat1
g2-2 g2 Treat1
g2-3 g2 Treat1
g2-4 g2 Treat1
g2-1 g2 Treat2
g2-2 g2 Treat2
g2-3 g2 Treat2
g2-4 g2 Treat2
g3-1 g3 Control
g3-2 g3 Control
g3-3 g3 Control
g3-4 g3 Control
g3-1 g3 Treat1
g3-2 g3 Treat1
g3-3 g3 Treat1
g3-4 g3 Treat1
g3-1 g3 Treat2
g3-2 g3 Treat2
g3-3 g3 Treat2
g3-4 g3 Treat2
