title: Development and application of a microarray meter tool to optimize microarray experiments.
abstract: BACKGROUND
  Successful microarray experimentation requires a complex interplay between the slide chemistry, the printing pins, the nucleic acid probes and targets, and the hybridization milieu. Optimization of these parameters and a careful evaluation of emerging slide chemistries are a prerequisite to any large scale array fabrication effort. We have developed a 'microarray meter' tool which assesses the inherent variations associated with microarray measurement prior to embarking on large scale projects.
  
  
  RESULTS
  The microarray meter consists of nucleic acid targets (reference and dynamic range control) and probe components. Different plate designs containing identical probe material were formulated to accommodate different robotic and pin designs. We examined the variability in probe quality and quantity (as judged by the amount of DNA printed and remaining post-hybridization) using three robots equipped with capillary printing pins.
  
  
  CONCLUSIONS
  The generation of microarray data with minimal variation requires consistent quality control of the (DNA microarray) manufacturing and experimental processes. Spot reproducibility is a measure primarily of the variations associated with printing. The microarray meter assesses array quality by measuring the DNA content for every feature. It provides a post-hybridization analysis of array quality by scoring probe performance using three metrics, a) a measure of variability in the signal intensities, b) a measure of the signal dynamic range and c) a measure of variability of the spot morphologies.
authors: Biomedical Genomics Microarray Facility (BIOGEM), La Jolla CA 92093, USA. rjdrouse@htresources.com
authors: Richard J D
authors: RJ
authors: Rouse
authors: Katrine
authors: K
authors: Field
authors: Jennifer
authors: J
authors: Lapira
authors: Allen
authors: A
authors: Lee
authors: Ivan
authors: I
authors: Wick
authors: Colleen
authors: C
authors: Eckhardt
authors: C Ramana
authors: CR
authors: Bhasker
authors: Laura
authors: L
authors: Soverchia
authors: Gary
authors: G
authors: Hardiman