Guide to Probe Logarithmic Intensity Error ( PLIER ) Estimation

The probe logarithmic intensity error (PLIER) method produces an improved signal (a summary value for a probe set) by accounting for experimentally observed patterns for feature behavior and handling error appropriately at low and high abundance. Resulting benefits include: · Higher reproducibility of signal (lower coefficient of variation) without loss of accuracy · Higher sensitivity to changes in abundance for targets near background · Dynamic weighting of the most informative probes in an experiment to determine signal This method was developed by building upon many of the concepts that have been published recently within the field of GeneChip microarray data analysis, including model-based expression analysis and robust multichip analysis. It also builds upon the summarization algorithm provided in Affymetrix Microarray Suite 5.0 (MAS 5) by taking into account the experimentally validated value of weighting feature intensities to determine an overall probe set summary. Similar to other model-based approaches, PLIER accounts for the systematic differences in intensity between features by including parameters describing these