I want to use the DESEQ2 tool to get my list of DE genes. I am comparing the values between control and mutant samples. (3 replicates for each case). I want to know what genes are DE in my mutant compared to my control. What should be my first factor level - control or mutant?
So should I have my first factor as control that has control count files and then in second factor have my mutant count files? OR
have my first factor as mutant that has mutant count files first, then in the second factor have my control count files?
the choice of factors will determine the interpretation of the results. So, if you choose the control samples as the first factor, a log2 fold change of -2 will mean that the expression of that gene will be lower in the mutants than in the control samples.
Thank you. I was following a course online on galaxy platform and they have said that the second factor is the baseline (control). Can you please let me know which is the right way?
as I was trying to explain, indeed it doesn’t matter; you just need to know how to interpret the output. You should just select a criterion for the interpretation of the results.