Fig. 4

Concordance of expression quantification between the libraries prepared with standard input protocols. a Scatter plots in a smoothed color density representation (top-right panel) and Spearman’s rank correlation coefficients (bottom-left panel) for all pairs of libraries using log₂(cpm + 1) values. b Unsupervised clustering of all the libraries using log₂(cpm + 1) values. Euclidean distance with complete linkage was used to cluster the libraries. c Principal component analysis (PCA) of all the libraries, using log₂(cpm + 1) values. The values for each gene across all the libraries were centered to zero and scaled to have unit variance before being analyzed. Circles and triangles represent control and experimental libraries, respectively (NuGEN, red; TruSeq mRNA, green; TrueSeq Total RNA, blue). For all analyses in Fig. 4, genes represented by fewer than 10 fragments in all the libraries were excluded