Figure 4

Evaluating TMM and fastlo normalization of tissue comparisons. A) Plots of log2(VMN/H) ratios (y axis) versus mean expression across all sample groups (x axis). N = 76,878 genes. Alignment along 0 horizontal is expected. Fitted loess lines are shown in blue. B) Histograms of VMN/H mean ratios. Even with peak at 0 indicates good normalization. C) Box plots of each sample group. Medians are expected to align along 0 with even distribution about the median across sample groups. RLE: Relative log ratio. D) Multidimensional scaling plots showing similarities between VMN (red) and H (black) sample groups. Samples show biologically relevant grouping by tissue and by season. BCV: biological coefficient of variation.