Defining signal thresholds in DNA microarrays exemplary application for invasive cancer.docVIP

BMC Genomics BioMedCentral BMC2002Genomics, 3 Methodology article x Defining signal thresholds in DNA microarrays: exemplary application for invasive cancer M Bilban*1,2, LK Buehler1, S Head1, G Desoye2 and V Quaranta1 Address: 1The Scripps Research Institute, Department of Cell Biology, 10550 North Torrey Pines Road, La Jolla, CA, USA and 2Clinic of Obstetrics and Gynecology, University of Graz, Auenbruggerplatz 14, A-8036, Austria E-mail: M Bilban* - mbilban@; LK Buehler - l.buehler@; S Head - shead@; G Desoye - gernot.desoye@kfunigraz.ac.at; V Quaranta - quaranta@ *Corresponding author Published: 17 July 2002 Received: 10 February 2002 Accepted: 17 July 2002 BMC Genomics 2002, 3:19 This article is available from: /1471-2164/3/19 ? 2002 Bilban et al; licensee BioMed Central Ltd. This article is published in Open Access: verbatim copying and redistribution of this article are permitted in all media for any non-commercial purpose, provided this notice is preserved along with the articles original URL. Abstract Background: Genome-wide or application-targeted microarrays containing a subset of genes of interest have become widely used as a research tool with the prospect of diagnostic application. Intrinsic variability of microarray measurements poses a major problem in defining signal thresholds for absent/present or differentially expressed genes. Most strategies have used fold-change threshold values, but variability at low signal intensities may invalidate this approach and it does not provide information about false-positives and false negatives. Results: We introduce a method to filter false-positives and false-negatives from DNA microarray experiments. This is achieved by evaluating a set of positive and negative controls by receiver operating characteristic (ROC) analysis. As an advantage of this approach, users may define thresholds on the basis of sensitivity and specificity considerations. The area und