Figure 2
From: Correlation test to assess low-level processing of high-density oligonucleotide microarray data
Correlations between the normalized expression values of the 5000 randomly selected pairs of genes. The most commonly used normalization procedure was chosen for each expression measure: global mean normalization for MAS5, quantile normalization for RMA, and invariant set normlization for MBEI, see Methods. Top: The distributions of the correlation coefficients are now centered at zero for all expression measures and data sets. Bottom: Summary curves plotting mean correlations versus median product of standard deviations for pairs of genes in non-overlapping intervals along the horizontal axis; 95% confidence intervals are shown as vertical bars. Normalization has removed most of the technical correlation (as seen in the reduced vertical scale compared to Figure 1), but there are still systematic relationships between correlations and standard deviations for RMA and MBEI, which are most pronounced for the Breast Cancer data set.