Best way to compare two different pipelines

Question

[Mozart]

Hello there, I carried out two different approaches to analyse the differential expression of my .fastq files. Now I want to compare these two results in order to consider similarity and divergences of these different approaches. I think the best way to do this is by creating a Venn diagram. Anyone with something "more unpredictable" to surprise my supervisors? :)

Answer 1

[BioinfGuru]

Does comparing how the results are different from each other really tell you anything valuable? You only need the methods "to consider similarity and divergences of these different approaches". I would think comparing how much the results of both approaches are different from the truth would be a better question to answer. This then allows you to conclude which pipeline is best.

tip: spike-ins

[cpad0112]

I second kenneth. Do a AUC.

[Mozart]

Thanks for your replies I will follow your advice.