Hello, I recently had a fairly straightforward dge analysis comparing two treatments with three biological replicates each. All samples were clones of the same plant and the tests were performed under the same growth conditions except for the treatment. DGE using the the glmQLFit and glmQLFTest commands resulted in 0 genes differentially expressed between the groups for a FDR threshold of 0.01.
I understand that the exact test will produce no genes with DE under two circumstances: 1) there is too much variation in the expression levels within groups and therefore the test estimates a high p.value which translates into no DGE and 2) both groups have actually very similar expression patterns even though the dispersion of the data is not too big.
How can I test which one of the above is the main reason driving the result of no differential genes? Is there any other explanation for that result that I have not considered?
Thank you for your help.
Juan D. Montenegro