About batch effect in separate library preparation for multiple samples tested on same day

Question

[yujunfhf]

Hi,

I am searching for explanation about batch effect. I found most computational methods are applied for batches that are from different labs/platforms/... But I am curious about the batch effect for samples from the same lab, and even same day of collection. These samples, like from different animals/ donors/ treatment groups, cannot be run in same batch if not using sample-multiplexing, so they are prepared as separate libraries and then sequenced. Is there batch effect that need to be concerned about? Or maybe this effect can be more easily corrected by computational method?

Thank you!

Answer 1

[jared.andrews07]

As with almost any assay, it's worth taking a look at the actual data before applying any batch correction or using it as a covariate during modeling. If I can't actually see/identify a batch effect via unsupervised methods, I generally don't account for it. Don't make it a problem if it isn't one.

[yujunfhf]

I see...Thank you!