Batch effects
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4 weeks ago
BioQueen ▴ 30

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!

Batch-effects transcriptomics • 371 views
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You have to download the raw dataset and correct for batch effects accordingly.

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

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

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29 days ago

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.

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