Zeitschrift für Proteomik und Bioinformatik
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Robust Detection of Outlier Samples and Genes in Expression Datasets

Ahmad Barghash, Taner Arslan and Volkhard Helms

Expression and methylation datasets are standard genomic techniques and an increasing number of computational methods are implemented to aid in analyzing the huge and complex amount of generated data. Such generated datasets often contain a sizeable fraction of outliers that cause misleading results in downstream analysis. Here, we present a comprehensive approach to detect sample and gene outliers in expression or methylation datasets. The core algorithms detected most outliers that were artificially introduced by us. Sample outliers detected by hierarchical clustering are validated by the Silhouette coefficient. At the gene level, the GESD, Boxplot, and MAD algorithms detected with f-measure of at least 83% the simulated outlier genes in non-intersected distributions. This combined approach detected many outliers in publicly available datasets from the TCGA and GEO portals. Frequently, some functionally similar genes marked as outliers turned out to have outlier observations in common samples. As such cases may be of special interest, they are labeled for further investigations. Expression and DNA methylation datasets should clearly be checked for outlier points before proceeding with any further analysis. We suggest that already 2 outlier observations are enough to label an outlier gene as they are enough to ruin a perfect co-expression. Besides, outliers might also carry useful information and thus functionally similar outliers should be labeled for further investigation. The presented software is freely available via github