Protocols for the Assurance of Microarray Data Quality and Process Control

Burgoon, L.D., Eckel-Passow, J.E., Gennings, C., Boverhof, D.R., Burt, J.W., Fong, C.J., Zacharewski, T.R.

Abstract

Motivation:

Microarrays represent a powerful technology that provides the ability to
simultaneously measure the expression of thousands of genes. However, it is
a multi-step process with numerous potential sources of variation that can
compromise data analysis and interpretation if left uncontrolled,
necessitating the development of quality control protocols to ensure assay
consistency and high data quality. In response to emerging standards, such
as the Minimum Information About a Microarray Experiment (MIAME) standard,
tools are required to ascertain the quality and reproducibility of results
within and across studies.

Results:

To this end, an intralaboratory quality control protocol for spotted
microarrays was developed using cDNA microarrays from in vivo and in vitro
dose-response and time-course studies. The protocol combines: 1) diagnostic
plots monitoring the degree of feature saturation, global feature and
background intensities, and feature misalignments with 2) plots monitoring
the intensity distributions within arrays with 3) a support vector machine
(SVM) model. The protocol is applicable to any laboratory with sufficient
data sets to establish historical high and low quality data.

Contact: tzachare@msu.edu

Supplementary Data

For full color plates showing examples of high and low quality microarrays, click here. [PDF]