Platform and sample specific biases. Bias patterns of gene expression levels in terms of log gene length, GC content and dinucleotide frequencies for 571 and 606 genes measured by both Taqman RT-PCR (expression levels in ΔCT unit) and RNA-Seq platforms (expression levels in log FPKM unit) and expressed above the detection thresholds in brain and UHR samples. The expression levels were rescaled to mean of 0 and standard deviation of 1 on Y-axes. In most bias plots, the fitted lowess curves for sequencing platform (blue and red) were separated from those from RT-PCR platform (green and black), which indicates platform specific biases. Only a few plots (e.g. for AG and GA dinucleotide frequencies) showed separation between brain samples and UHR samples, which indicates sample specific biases.
Zheng et al. BMC Bioinformatics 2011 12:290 doi:10.1186/1471-2105-12-290