Scatter Plot from Scientific Research

Scatter plots of PCA on RNA-seq data after batch correction from replicates of the Quartet RNA reference materials (marked in colors) in the 21 batches (marked in shapes). Expressions in log 2 FPKM were used as before batch-correction datasets. Ratio-based expressions (which referred to converting expression profiles to gene-wise relative-scale profiles within each batch) were used to correct batch effects. Ratio-based expressions were obtained by subtracting log 2 FPKM by the mean of log 2 FPKM of the three replicates of D6 in the same batch. We used a multi-batch RNA-seq dataset, including 168 RNA-seq libraries from the RiboZero protocol and 84 RNA-seq libraries from the PolyA protocol. Plots were color-coded by sample groups and shaped by batches.

DOI