Quality Assessment of Exon and Gene Arrays
Revision Date: 2007-04-06
Revision Version: 1.1
Affymetrix GeneChip® Gene and Exon Array Whitepaper Collection:
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Quality Assessment of Exon and Gene Arrays
I. Introduction
In this white paper we describe some quality assessment procedures that are
computed from CEL files from Whole Transcript (WT) based arrays such as the
Human Exon 1.0 ST Array and the Human Gene 1.0 ST Array. Some of the
methods detailed here are described in Chapter 3 of the Bioconductor
monograph (Gentleman et. al. 2005).
Many of the quality assessment procedures considered here entail computing
summary statistics for each array in a set of arrays and then comparing the level
of the summary statistics across the arrays. Therefore it is assumed that the user
has a set of arrays that would normally be analyzed together to address
substantive biological questions.
The quality assessment procedures discussed in this this white paper focus on
using various metrics to identify outlier arrays within the data set. These metrics
can identify outliers; however it is impossible to provide hard and fast rules
(specific thresholds) as to which arrays to flag as outliers. Such rules need to be
developed in the context of particular applications with specific types of samples,
combined with balancing the cost of repeating experiments and the cost of
drawing wrong conclusions.
II. Quality Assessment Software
This white paper focuses on quality assessment metrics and graphs available
through the Expression Console™ software(EC) which is freely available from
http://www.affymetrix.com. EC supports probe set summarization, calculation of
various quality assessment metrics, and CHP file generation. EC also supports a
variety of visualization and graphing tools to facilitate data quality assessment.
EC replaces the previously supported Exon Array Computational Tool (ExACT).
It should also be noted that the probe set summarization methods available in EC
are implemented in the