PLIER

PLIER (Probe Logarithmic Intensity Error Estimation) is a multi-array normalization method developed by Affymetrix that produces an improved signal by accounting for experimentally observed patterns in feature behavior and handling error at the appropriately at low and high signal values. When selected, ArrayStar adjusts the probe intensity data in two steps:

1)  Data across all of the chips is normalized using the selected normalization method:

•      Quantile: Adjusts the probe intensity values so that the distribution is the same across all arrays.

•      Sketch Quantile: Adjusts the probe intensity values so that the distribution is the same across all arrays using only a subset of the signal values, so that it uses less memory than full Quantile normalization.

•      Global Median: Scales the probe intensity values so that the median per array is the same across all arrays. Each experiment in your project will be scaled so that they all have the same median signal value.

•      None: No adjustments will be made to the probe intensity values.

2)  Probe data are summarized into gene level signal values using the PLIER algorithm and the selected PLIER background adjustment method:

•      Perfect Match: This method only considers the perfect match probes. This is most useful when the background is assumed to be minimally variable, as when using identical tissues, organisms, or cell lines.

•      Perfect Match-Mismatch: This method subtracts the value of the mismatch probes from the perfect match probes. This is the most conservative approach and is the default option for 3’ expression chips. This option is disabled when importing Affymetrix whole-transcript chips as there are no mismatch probes on that chip type.

PLIER normalization is only available for Affymetrix .cel files.

For additional information on the PLIER method, please consult this Technical Note from Affymetrix.