I want to apply ComBat function in the sva package to an RNA-Seq dataset containing FPKM values. I first added 1 to all counts and then log-transformed the data followed by calling the ComBat function. However, I have no actual zero counts in the cleaned data while there were many zeros in the original data. This is expected since ComBat standardizes the data. All zeros are mapped to values between -0.36 and 4.45 (after exp-transformation and subtracting 1), and there are no exact zeros. However, it is kind of weird to have negative values and also no zero counts in the RNASeq data. So, my question is "what is the best way to use ComBat on RNA-Seq data?". Thanks.