I have a RNA-Seq dataset and want to test differential gene expression with DESeq2 for just some of the genes but for many different phenotypes. Now I have 3 questions:
- I have to give DESeq all the genes and then only subset the results to the genes of interest, correct?
- The most time-consuming step seems to be the dispersion estimation. Is this dependent on the design matrix, i.e. the phenotype? Or is there a way to correct for dispersion once and then perform the differential expression test for multiple phenotypes on the same normalized dataset?
- If 2 is possible: Can I do the testing for only some of the genes after I normalised the dataset with all the genes?