Hello everyone, Quick explanation. We have a traditional experiment setup with plant clones. We are comparing two treatments with three biological repeats each. So in total 6 libraries. After running the DGE pipeline recommended in edger I have found 0 genes DE.
Nos before I draw a conclusion I'd like to be sure why I found no DGEs. From what I understand, there are mainly two reasons: 1) the expresión patterns are too disperse and therefore the exact test could not find any significant gene even though there might be some or; 2) the two groups indeed have very similar expression patterns and that's why there are no DGEs.
So basically I want to see if the dispersion of the data is the main reason for no DGEs or not. I'm not sure how to interpret the BCV plot and how to deduce the level of variability for each gene from.that plot. Do you have any other suggestion as to why the there might be no genes DE or how to test the reasons for that result?
Can you plot and show the distribution of p-values for your genes? Is it flat?