JSM 2005 Online Program

Abstract #304722

This is the preliminary program for the 2005 Joint Statistical Meetings in Minneapolis, Minnesota. Currently included in this program is the "technical" program, schedule of invited, topic contributed, regular contributed and poster sessions; Continuing Education courses (August 7-10, 2005); and Committee and Business Meetings. This on-line program will be updated frequently to reflect the most current revisions.

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Activity Number:	514
Type:	Contributed
Date/Time:	Thursday, August 11, 2005 : 10:30 AM to 12:20 PM
Sponsor:	Biometrics Section
Abstract - #304722
Title:	Another Look at PLIER
Author(s):	Karla Ballman*+ and Terry M. Therneau
Companies:	Mayo Clinic and Mayo Clinic
Address:	Cancer Center Statistics KA1A, Rochester, MN, 55905, United States
Keywords:	Affymetrix microarrays ; error model
Abstract:	Probe Logarithmic Intensity ERror (PLIER) is one of the methods available in the new release of the Affymetrix software for producing a gene expression measure (intensity value) based on the observed values of the perfect match (PM) and mismatch (MM) probe pairs within the probeset corresponding to the gene. PLIER performs better than MAS 5.0 and relatively well with respect to other commonly used methods on publicly available spike-in datasets using the Affycomp metrics. One of the steps in the derivation of the algorithm is the assumption that the MM error (multiplicative error) for a given spot is equal to the reciprocal of the PM error for that spot. This error model is not biologically intuitive, particularly because PM/MM pairs are adjacent on the chip. To understand how the PLIER method works, we explored the performance of the proposed error metric. We found that by appropriately scaling the data, the PLIER solution is well approximated by the harmonic mean of the PM values, along with an attenuation term based on the average MM/PM ratio.

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