Comparing RNA-Seq and Agilent microarrays for detecting genes expressed in the liver and differentially expressed by TCDD. (A) RNA-Seq reads were aligned to mouse genome GRCm38 (release 74) and subsampled to represent 3–5 independent biological replicates. The number of differentially expressed genes (DEGs) was determined under varying |fold change| and P1(t) criteria. (B) Microarray features were examined for DEGs under varying |fold change| and P1(t) criteria. (C) RNA-Seq and microarray detected genes (yellow boxes) were examined for common and unique detected genes and DEGs. (D) Distribution of log2 (fold change) and (E) P1(t) values (P1 (t) ≥ 0) in RNA-Seq (blue) and Agilent (pink) datasets.