Bias plots for MAQC data (Procedure 1, gene-level). Genes were grouped into bins according to log gene length, GC content, and dinucleotide frequencies, and the median expression levels in log(FPKM) units versus median bias factors were plotted for MAQC2 brain and UHR samples before and after GAM correction. Each bin contains 500 genes. Data were processed by Procedure 1. This data set showed strong linear relationship between expression levels and gene length, GC content and dinucleotide frequencies that are related to GC content (i.e. AA, AT, TA, TT, GG, GC, CG, CC). Moreover, the patterns from two different biological samples (brain and UHR) were very similar. After GAM correction, the bias patterns diminished.