Having had personal communication with Dr. Evan Johnson on this very question, I am quoting his email response. > So my question is: Are there any reasons why using ComBat with RNA-seq data is not legit? Here is what Evan had to say: "For batch effects, if the sample sizes are large, say around 10 per batch or more, ComBat and SVA will work fine regardless of whether they are on count data or not. For cases with 50-100 per batch, ComBat and SVA will work extremely well and will be somewhat optimal. Basically this is due to the Central Limit Theorem. For small batch size, ComBat and SVA are still valid, but there may be some research that can be done here." Hope that helps, Christopher Conley Graduate Group of Biostatistics UC DAVIS