Objective method of comparing DNA microarray image analysis systems.
Many image analysis systems are available for processing the images produced by laser scanning of DNA microarrays. The image processing system takes pixel-level intensity data and converts it to a set of gene-level expression or copy number summaries that will be used in further analyses. Image analysis systems currently in use differ with regard to the specific algorithms they implement, ease of use, and cost. Thus, it would be desirable to have an objective means of comparing systems. Here we describe a systematic method of comparing image processing results produced by different image analysis systems using a series of replicate microarray experiments. We demonstrate the method with a comparison of cDNA microarray data generated by the UCSF Spot and the GenePix image processing systems.
Korn
Edward L
EL
Biometric Research Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA. korne@ctep.nci.nih.gov
Habermann
Jens K
JK
Upender
Madhvi B
MB
Ried
Thomas
T
McShane
Lisa M
LM
D000465:Algorithms; D019544:Equipment Failure Analysis / Q000295:instrumentation* / Q000379:methods / Q000592:standards; D007090:Image Interpretation, Computer-Assisted / Q000295:instrumentation* / Q000379:methods / Q000592:standards; D018613:Microscopy, Confocal / Q000295:instrumentation* / Q000379:methods / Q000592:standards; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation* / Q000379:methods* / Q000592:standards; D010363:Pattern Recognition, Automated / Q000379:methods* / Q000592:standards; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D012815:Signal Processing, Computer-Assisted