Batch effect

[Amative]

Hello everyone,

What is batch effect in rna-seq? How to check if one has it?
Any tools or links or documents would be great!

Thanks in advance

[swbarnes2]

Batch effect means that if I prep three samples, and a co-worker preps replicates of the same three samples, (Or I can prep three samples one day, and prep replicates of them the next day) you can look at the data, and say: "These three samples were prepped in one batch, and these three were prepped in another batch". Not good.

So you should do some trial experiments in your lab, to see how large batch effects are in your lab. It mostly depends on how careful the people prepping the samples are, some batch effect is likely inevitable. When possible, all the samples of a particular project should be all prepped together, by the same person, to minimize possible batch effects.

[PeteH]

You might like to have a read of this paper as a starter - Tackling the widespread and critical impact of batch effects in high-throughput data
Pete

[Amative]

Thanks a lot, I believe I got the idea
The paper is super helpful