Hi Emily, See below: On Apr 16, 2013, at 2:03 PM, Emily Chen wrote: Hello, My name is Emily Chen and I’m a graduate student at the University of Southern California. I have human biological tissue RNA-Seq data and am issue in using ComBat as I’ve heard that it can control for effects such as positive toxicology results and age. Is this true? Let me clarify what you are asking: Are you trying to control for tox and age while adjusting for batch, or are you trying to remove/adjust out the tox or age effects? If the former, this is one of the greatest strengths with ComBat. So Just include these in the model matrix and ComBat will to the rest. If the latter, then you should be using EdgeR and include an age and tox effect. What is your variable of interest and what is the relationship between this interest variable and tox/age? What is your experimental design and batching information, etc? And can this be used with RNA-Seq data and not just array data? RNA-seq might be a problem, but then again it might not. It depends on the size of your dataset how you are processing the data. How big is your sample size? How are you processing the data (e.g. RPKM, FPKM, raw count, normalization, etc)? Thank you, Emily [[alternative HTML version deleted]]