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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.
