The order used in common practce? batch effect removel and normalization
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@catechize2learn-21902
Last seen 2.2 years ago

Hi!

I am aware of an old post at biostars: In Which Order Use Normalization And Batch Effects Removal? https://www.biostars.org/p/83531/

I think many visitors to this BioC forum perform these procedures routinely. I need a general advice on the order of these procedures in microarray analysis.

Thanks.

normalization batch effect • 462 views
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chris86 ▴ 400
@chris86-8408
Last seen 3.0 years ago
UCL, United Kingdom

I'd normalise first to remove your technical variation within batches, if this was RNA-seq then some samples might have way more reads in than others and that would need correcting for. Then batch is like differences between certain labs and operators etc, so that can be done afterwards.

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Ok thanks. What you advised is similar to what I found at biostars, but it was a little against what I had in my mind.

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