MAQC-2 dataset: p-value vs. GC-content. Median unadjusted p-value (log10) for each GC-content stratum, for microarray and RNA-Seq UHR vs. Brain DE analysis (11,081 genes detected by RNA-Seq and present on the Affymetrix chip). The figure shows that the GC-content bias is technology-related and that full-quantile within-lane normalization reduces the dependence of RNA-Seq p-values on GC-content.
Risso et al. BMC Bioinformatics 2011 12:480 doi:10.1186/1471-2105-12-480