AbstractBackgroundThe Random Forest (RF) algorithm for supervised machine learning is an ensemble learning method widely used in science and many other fields. Its popularity has been increasing, but relatively few studies address the parameter selection process: a critical step in model fitting. Due to numerous assertions regarding the performance reliability of the default parameters, many RF models are fit using these values. However there has not yet been a thorough examination of the parameter-sensitivity of RFs in computational genomic studies. We address this gap here.ResultsWe examined the effects of parameter selection on classification performance using the RF machine learning algorithm on two biological datasets with distinctp/nratios: sequencing summary statistics (lowp/n) and microarray-derived data (highp/n). Here,p,refers to the number of variables and,n, the number of samples. Our findings demonstrate that parameterization is highly correlated with prediction accuracy and variable importance measures (VIMs). Further, we demonstrate that different parameters are critical in tuning different datasets, and that parameter-optimization significantly enhances upon the default parameters.ConclusionsParameter performance demonstrated wide variability on both low and highp/ndata. Therefore, there is significant benefit to be gained by model tuning RFs away from their default parameter settings.