cross dataset analysis_RNA Seq

Question

[sa1987]

hi

I am using the RNA seq datasets. Can we use control from one dataset and treated from other datasets?. If yes should we use normalizing techniques?

Answer 1

[ATpoint]

No, you cannot. Please browse this forum for similar threads, e.g the keyword batch effect is of help. There are countless threads with the same question. The crux is that you cannot distinguish whether an effect is due to the biological difference (which you are looking for) or the differences between labs, kits, sequencing etc. (technical batches).