Correction of Spatial Bias in Oligonucleotide Array Data
Effect of correction on DEG detection power. Receiver operating characteristic (ROC) curves generated by the R/bioconductor package affycomp, plotting sensitivity as a function of (1 – specificity), as computed in data obtained with RMA (all default parameters) after pretreatment with each of the spatial correction methods (or none) for (a) low-, (b) medium-, and (c) high-concentration spike-in genes. See [6, 43] for details. At low and medium concentrations, pyn performs the best; at all concentrations, Upton-Lloyd performs the worst by a large margin; CPP and LPE have virtually no effect, with the exception of CPP degrading results at high concentration.