Batch effects

Question

[BioQueen]

Hi!

I'm new at bioinformatics and I'm working with a project where I combine several datasets from GEO. I retrieve the data from GREIN(GEO RNA-seq Experiment Interactive Navigator) which has processed all the datasets in the same way. They provide raw and normalised data.

My question is when and how do I correct for batch effects?

Thanks a lot!

[Hyper_Odin]

You have to download the raw dataset and correct for batch effects accordingly.

[BioQueen]

Ok, thanks so I can't do it after normalization?

[Hyper_Odin]

I am sorry for the confusion, you can perform batch effect correction even after normalization!

Answer 1

[swbarnes2]

It's always safest to get raw data and normalize it yourself.

If one dataset is control, and the other is not, there is no magic way to correct for batch effects.