Figure 2
From: Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data
Hybridization bias. Sequence-specific dependency of reporter intensities before (top), after normalization using rMAT (middle) resp. after rank-percentile normalization and reference subtraction (bottom). Left column: Boxplots of probe intensity distributions. Probes are grouped according to the GC-content in their sequence. The median intensity increases with rising GC-content. Right column: Position-dependent mean probe intensity. Each letter corresponds to the mean intensity of all probes that contain the corresponding nucleotide in the respective position.