I am using DESeq2 to analyze differential expression between two conditions (RNAseq, 3 replicates each). When playing around with different fit types as parameters for the DESeq() function I found that the default (parametric) fit results in 29 genes with adjusted p-values below my threshold while the local fit gives me 153.
This lead me to the question which of the two I should use and if there is an objective way to make this decision. I obviously don't want to choose one just because it gives me more/better results.
It would be great if you could give me some suggestions as to how this decision should be made? If at all possible, I'd like to find a way to assess the fit in a more quantitative way than visual inspection.
Thanks in advance,