2014/1/30: In EBSeq 1.3.3, the default setting of EBTest function will remove low expressed genes (genes whose 75th quantile of normalized counts is less than 10) before identifying DE genes. These two thresholds can be changed in EBTest function. We found that low expressed genes are more easily to be affected by noises. Removing these genes prior to downstream analyses can improve the model fitting and reduce impacts of noisy genes (e.g. genes with outliers).