Figure 6

One-way ANOVA of technical replicates. Three patient samples (#25, #26, and #27) from distinct leukemia subtypes were analyzed in three independent technical replicates for each method A, B, and C leading to a dataset of 27 gene expression profiles. (A) The graph represents false discovery rate (FDR) values based on One-way Analysis of Variance (ANOVA) results. For each preparation method the absolute number (left x-axis) and percentage of differentially expressed genes (right y-axis) between the various leukemia subclasses is given. The x-axis is representing multiple percentages of false discovery rates (%FDR). Method A: red line, method B, blue line, method C, green line. The vertical line is drawn at a FDR of 0.001 (0.1%). (B) Venn diagram representing the absolute number of overlapping differentially expressed genes for the three methods used. The representation is based on a series of filters: present calls, fold-change, and FDR of 0.001 (0.1%). For example, n = 7,728 genes are found to be consistently differentially expressed between the various leukemia subclasses when comparing method A to B, method A to method C, and method B to method C. As a second example, n = 2,107 genes are exclusively found to be differentially expressed when using sample preparation method A. Alternatively, n = 1,274 genes are detected to be differentially expressed by both method A and method C, but not by method B. (C) Summary table representing the percentages of overlapping differentially expressed genes for the three methods used. The first line represents the comparisons of method A to method B or method C. The second line represents the comparisons of method B to method C or method A. The third line represents the comparisons of method C to method A or method C.