Correction of Spatial Bias in Oligonucleotide Array Data

Figure 4

Effect of correction on reproducibility across replicate arrays. Standard deviation of log expression index of probe sets across replicate arrays as a function of mean log expression, as computed in data obtained with RMA (all default parameters) after pretreatment with each of the spatial correction methods (or none). pyn performs best, resulting in an increase in reproducibility notably for low-expression genes, while Upton-Lloyd deteriorates data for low-expression genes, and CPP and LPE have virtually no effect.