Which method could be used for cross normailizing microarray samples from different platforms namely (Affmetrix, Agilent,Illumina..) ?
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9.8 years ago
macmath ▴ 170

Received data from Affmetrix

New data in Agilent and other in Illumina

How to normalize these data so that we can reduce platform batch effect

microarray normalization • 2.4k views
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9.8 years ago
Manvendra Singh ★ 2.2k

There is an algorithm from ComBat which is here also in sva package from bioconductor here.

When I analyze I just pick single value for each gene on their mean, I merge normalized data from different platforms . ( e.g. "data")

I normalize merged data on their quantiles

by

library(limma)
normalized.data <- normalizeQuantiles(data)

hth

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Thank you for your suggestion Manvendra Singh

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This package has problems in regard to bias in expression values. Are you aware of some other tools?

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Which tool?

ComBat is good for expression bias

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