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ReliefSeq: A Gene-Wise Adaptive-K Nearest-Neighbor Feature Selection Tool for Finding Gene-Gene Interactions and Main Effects in mRNA-Seq Gene Expression Data

Figure 6

Main effect simulation results comparing gene-wise adaptive-k ReliefSeq, edgeR, and DESeq.

Average ranks of the 96 main effect genes simulated in each data set with a total of 16,920 genes for Relief-F with optimized k nearest neighbors, edgeR, and DESeq. The results are split into four panels based on fold change (FC) on the raw scale. The horizontal axis shows the 96 simulated main effect genes, ordered left to right from high to low main effect strength, and labeled by the combination of negative binomial parameters (θ:µ) of the main effect gene. Each point is the average rank across n = 1000 replicate simulations (vertical axis).

Figure 6