Hi,
Currently I am replicating a few DEG analysis for publicly available datasets. However, my results are not that close to original publications. For example, I got genes related to immune response just like in the original paper. However, genes are not the same. Since I found similar pathways, I thought maybe DEG analysis is not that reproducible? Thoughts, experiences?
When you say you are "replicating" the DEG analysis do you mean:
using their data and their methods in an attempt to get the same results as them.
Using their data but your methods
Generating a new datasets (making new RNA libraries etc) that should be a replicate of theirs?
Ah, I forgot it. Thanks! I mean 2.