Figure 5

Scaling of microarray probes by RNA-Seq leads to improved biological reproducibility. A) Strategy to convert intensity levels of all probes to sequencing scaled microarray intensities (SSMIs) using samples from brain 2. SATB2 is shown as an example. 5^th and 95^th quantiles (red dots) are compared between methods, and microarray intensities are scaled linearly such that these quantiles align. Grey and black dots show expression of a sample in brain 2 for both methods before and after scaling, respectively. Inset shows the range of slope (m) and intercept (b) parameters across all probes (25%, 50%, and 75% quantiles shown in bold; 5% and 95% quantiles shown in light lines or enumerated if off the plot). (B -C) After scaling (black dots), all samples in brain 1 show markedly improved between-method correlation of absolute expression levels compared with before (grey dots). This result holds for all 115 samples in brain 1 (B). A single example is shown in C (corresponding to the arrow in B; labeling as in Figure 2B). Diagonal dotted line indicates perfect agreement of absolute expression levels (y = x). D) SSMIs show improved reproducibility between methods based on between-method (left; * = compare with Figure 2G) and between-brain (right; ^ = compare with Figure 2E) differential expression measures (compare with Figure 4C). The blue line indicates the between-brain correlation as measured by RNA-Seq (Figure 2F), which is now only slightly higher (ΔR=0.02) than in microarray.