Question

Removing batch effect from microarray data

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arisarkar88 ▴ 40

@arisarkar88-11464

Last seen 9 months ago

Los Angeles

Hello,

I have multiple cel files corresponding to affymetrix platform. How to remove batch effect from these .cel files and then go for normalization of these?

removebatcheffect() microarray affymetrix microarrays • 2.2k views

ADD COMMENT • link updated 7.1 years ago by Aaron Lun ★ 28k • written 7.1 years ago by arisarkar88 ▴ 40

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I suggest you use R limma for this. You can read the manual wherein they describe exactly how to analyze this.

ADD REPLY • link 7.1 years ago b.nota ▴ 360

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OK..I will definitely go through it

ADD REPLY • link 7.1 years ago arisarkar88 ▴ 40

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Are you saying that you have celfiles from multiple different Affy platforms? Or are you simply saying that you have multiple celfiles from AN Affymetrix platform?

ADD REPLY • link 7.1 years ago James W. MacDonald 65k

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Yes, I have multiple celfiles from an affymetrix platform.

ADD REPLY • link 7.1 years ago arisarkar88 ▴ 40

score 1 · Answer 1 · 2017-03-07

You should normalise first and then do batch correction on the normalised (log-)intensities. There are also other steps to consider like background correction and (if you intend to do a DE analysis) filtering to remove low-abundance genes. Read the limma user's guide for more details and worked examples, though you should also read the affy manual if you're dealing with Affymetrix data.