Figure 3

Schematic diagram of study workflow , including probe set filtering steps and statistical test strategies for detecting significant single genes and pathways. The probe intensities measured in 209 hybridized Affymetrix HG-U133 plus 2.0 arrays were normalized by Robust Multichip Average followed by a baseline correction step. Probes marked ‘Presence’ in fewer than four arrays in each group (because for Week 12 placebo group, only two positive responders were included, probes with two valid measurements were kept) were removed. Probes corresponding to control or less well-defined genes, and duplicated probes were removed. Genes with low FCs; i.e., within 1 standard deviation (denoted by σ) for a total of L (~7500) genes also were removed, as most of them were not likely to be differentially expressed to a statistically significant extent. The remaining genes were tested by the ordinary Student’s t-test, and genes with P values < 0.05 were used for pathway analysis. In total, 3698, 3532, 3328, and 3405 genes were tested for the Week 8 TPM, Week 8 placebo, Week 12 TPM, and Week 12 placebo groups, respectively.