I have a RNA-seq experiment with paired-end reads from 6 samples. Each sample is a different genotype (5 different mutants + 1 wt control) and each has two replicates. I have tried running DESeq2 two different ways leading to vastly different results.
- 1 Factor = genotype, then 6 factor levels (1 level for each genotype) I set this option "Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor" to yes
- Several pairwise comparisons, for example( 1 Factor = genotype, factor level 1=genotype1, factor level 2=wt) In this 2nd case, I ran deseq2 5 times doing just a pairwise comparison with each mutant to wt.
Am I doing this analysis appropriately? The results I get are very different.