Figure 6

Cross-dataset Latent ProbeSet Structure. Cross-dataset Latent ProbeSet Structure using BaFL produced values. Two-dimensional projection calculated with spectral method of Higgs et al., as derived from the LaFon method. Sample correlation values using differential expression (DE) gene responses were used as input. Each symbol represents a ProbeSet, both color and direction of arrow indicate change: up (gray)- or down (black)-regulation, or not significantly different (white). Panel A: the 940 ProbeSets that are DE in both experiments. These ProbeSets pass BaFL pipeline criteria and are categorized as DE according to both RMA and dCHIP output (but not always in the same direction). Dark Grey upward-pointing arrows indicate up-regulated genes in the adenocarcinoma samples relative to normal samples. Black downward-pointing arrows indicate down regulation in adenocarcinoma samples relative to normal samples. Open white circles in Panel A indicate ProbeSets that BaFL does not interpret as significantly differentially expressed, while the other methods do. Bottom graph: the subset from panel A of the 325 ProbeSets predicted to be significantly DE by BaFl. The tables from which the graphs are made are provided in the Supplementary Materials Web site for the article, Latent Structure [19].