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Thread Subject:
Adjusting batch effects in microarray data using empirical Bayes methods

Subject: Adjusting batch effects in microarray data using empirical Bayes methods

From: Frank Sabouri

Date: 24 Aug, 2010 00:22:04

Message: 1 of 1

Batch effects or non-biological experimental variation are commonly observed across multiple batches of microarray experiments. The ability to combine microarray data sets is advantageous to researchers to increase statistical power to detect biological phenomena from studies where logistical considerations restrict sample size or in studies that require the sequential hybridization of arrays. We need to combine datasets; therefore, we should adjust batch effects. There are proposed parametric and nonparametric empirical Bayes frameworks called “combat” for adjusting data for batch effects that is robust to outliers in small sample sizes and performs comparable to existing methods for large samples.

Please let me know whether there is a MATLAB toolbox that allows me to remove these batch effects from the data as “combat” does.

Frank

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