Figure 4

Probes chosen by RNA-Seq show improved reproducibility metrics. A) Example gene (ZFR2) with different probes showing the "worst" between-method correlation (left), the "highest" average expression (center) and the "best" between-method correlation (right). Each plot shows the expression level of a microarray probe (y-axis) and the corresponding gene TPM value as measured by RNA-Seq (x-axis). Each dot represents a single sample in our training set (brain 2). Two of these probes would be filtered out as "low quality" using our metric. B) Between method (left) and between-brain (right) measures of differential expression correlation when defining microarray genes based on the worst, highest, and best probes (left three bars). Note that correlations in the "highest probes" bars come directly from Figure 2G (*) and Figure 2E (^). The other two bars correspond to the subset of best probes that pass (green) and fail (red) quality control based on our filtering strategy, respectively. Note that the best passing probes have the highest reproducibility. C) Genes with low expression are more likely to fail than genes with moderate to high expression. Genes were binned based on expression levels (x-axis) and the number of passing and failing probes is shown for each bin (y-axis). 91% of genes with log2(intensity) > 3 passed, compared to only 47% with lower expression.