Figure 3. Principle component analysis (PCA) to assess the library preparation batch effect.

Each sample is denoted by a circle or triangle. (a) A 2D PCA plot of all samples shows no separation between the two library preparation batches, i.e., Lib1 and Lib2. The analysis was done with the top 10,000 genes selected by average expression level ranking. (b) A 2D PCA plot of all 3 technical replicas for each of the six samples (3 treated by aflatoxin B1 (AFL) and 3 matched controls (CTL)). (c,d) Two bar charts plot the percentage of variance explained by each of the top principle components for the corresponding PCA plots (a,b).