Removing batch effect from microarray data
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@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 • 1.4k views
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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.

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OK..I will definitely go through it

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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?

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Yes, I have multiple celfiles from an affymetrix platform.

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Aaron Lun ★ 27k
@alun
Last seen 17 hours ago
The city by the bay

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.

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