How to estimate batch effect in microarray gene expression data?

Question

[chengzhao41]

I have microarray gene expression data and their labels for a supervised tasks and some sample info, how can I estimate the batch effect?

[Manvendra Singh]

what kind of gene expression data?

RNA-seq or microarray?

batch effect usually arises during analysis of cross-platform datasets

[chengzhao41]

Microarray. I have updated the question

[Manvendra Singh]

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.

Answer 1

[Ashutosh Pandey]

If you are looking for a tool then COMBAT is the answer.