Question: How to estimate batch effect in microarray gene expression data?
0
gravatar for chengzhao41
5.1 years ago by
chengzhao4190
Canada
chengzhao4190 wrote:

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

ADD COMMENTlink modified 5.1 years ago • written 5.1 years ago by chengzhao4190

what kind of gene expression data?

RNA-seq or microarray?

batch effect usually arises during analysis of cross-platform datasets

ADD REPLYlink written 5.1 years ago by Manvendra Singh2.1k

Microarray. I have updated the question

ADD REPLYlink written 5.1 years ago by chengzhao4190

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.

ADD REPLYlink written 5.1 years ago by Manvendra Singh2.1k
0
gravatar for Ashutosh Pandey
5.1 years ago by
Philadelphia
Ashutosh Pandey11k wrote:

If you are looking for a tool then COMBAT (http://www.bu.edu/jlab/wp-assets/ComBat/Abstract.html) is the answer.

ADD COMMENTlink written 5.1 years ago by Ashutosh Pandey11k
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