JSM 2005 - Toronto

Abstract #303583

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Legend: = Applied Session, = Theme Session, = Presenter
Activity Number: 34
Type: Contributed
Date/Time: Sunday, August 7, 2005 : 2:00 PM to 3:50 PM
Sponsor: Biopharmaceutical Section
Abstract - #303583
Title: Cosmetics in Microarray: A Program for Automatically Masking Blemishes in Affymetrix Chips
Author(s): Mayte Suarez Farinas*+ and Maurizio Pellegrino and Knut M. Wittkowski and Marcelo O. Magnasco
Companies: The Rockefeller University and The Rockefeller University and The Rockefeller University and The Rockefeller University
Address: 1230 York ave, New York, NY, 10021, United States
Keywords: microarrays ; mask ; defects ; chip analysis ; preprocessing ; R packages
Abstract:

Microscopists are familiar with blemishes that fluorescence images can have due to dust and debris, glass flaws, uneven distribution of fluids, or surface coatings. Microarray scans show similar artifacts that affect the analysis, particularly when trying to detect subtle changes in a small set of genes. However, most blemishes are hard to find by the unaided eye, particularly in Affymetrix GeneChip arrays. We present a method harnessing the statistical power provided by several chips that "harshlight" these blemishes, rendering them evident. Furthermore, we develop an R package for their automatic detection; implementation includes image recognition routines for different types of defects and masking before further preprocessing. Experiments attempting to assess subtle expression changes should be carefully screened for blemished chips. By utilizing topological information for identification and elimination before model-based analyses, the proposed method prevents faulty data from confounding the process of background correction, normalization, and summarization, thereby presenting investigators with a novel robust approach to detect blemishes on microarrays.

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Revised March 2005