How to estimate batch effect in microarray gene expression data?
I have microarray gene expression data and their labels for a supervised tasks and some sample info, how can I estimate the batch effect?
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Ram
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chengzhao41
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chengzhao41
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If you are looking for a tool then COMBAT is the answer.
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Ashutosh Pandey
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what kind of gene expression data?
RNA-seq or microarray?
batch effect usually arises during analysis of cross-platform datasets
Microarray. I have updated the question
so you have microarray datasets from different platforms.
you can normalize their quantile wrt reference sample , and batch effect would be removed . Removed batch effect is estimation of batch effect.