Question: The order used in common practce? batch effect removel and normalization
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gravatar for catechize.2.learn
4 weeks ago by
catechize.2.learn10 wrote:

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.

ADD COMMENTlink modified 4 weeks ago by chris86380 • written 4 weeks ago by catechize.2.learn10
Answer: The order used in common practce? batch effect removel and normalization
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gravatar for chris86
4 weeks ago by
chris86380
UCL, United Kingdom
chris86380 wrote:

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.

ADD COMMENTlink written 4 weeks ago by chris86380
1

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.

ADD REPLYlink written 4 weeks ago by catechize.2.learn10
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