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Simultaneous dimension reduction and adjustment for confounding variation #MMPMID27930330
Lin Z; Yang C; Zhu Y; Duchi J; Fu Y; Wang Y; Jiang B; Zamanighomi M; Xu X; Li M; Sestan N; Zhao H; Wong WH
Proc Natl Acad Sci U S A 2016[Dec]; 113 (51): 14662-7 PMID27930330show ga
With the advancement in high-throughput technologies, analyzing high-dimensional data has become a common task. Dimension reduction methods have been applied to visualize and identify dominant patterns in high-dimensional data. Confounding factors, commonly observed in high-throughput biological experiments, can affect the performance of these methods, and other downstream analysis. Here, we develop a method by coupling dimension reduction with the adjustment for confounder effects. Our method is able to capture the underlying patterns, as demonstrated by a human brain exon array dataset, a model organism ENCODE RNA sequencing dataset, and simulations.