I've been struggling with my 2-way ANOVA analysis. I have 4 genotypes, lets name them A, B, C and D, and 3 time points: 0, 1 and 3. I need to test for time specific and genotype specific responses in my RNAseq data. I am quite new to bioinformatic field. How do I specify groups, do I use normalized counts or row counts? And how to actually do 2-way ANOVA analysis? All I found so far, was one-way...
Any help will be appreciated.