ELB-Q: A new method for improving the robustness in DNA microarray image quantification
Document Type
Article
Publication Date
9-1-2007
Abstract
Reliable and robust quantification of signal intensities is a critical step in microarray-based biomedical studies. However, traditional techniques for microarray image processing would face significant challenges if the number of pixels used for the quantification of the local background and the foreground decreases dramatically. We have developed a new method, ELB-Q, which, by design, is well suited for the image quantification of microarrays with very high density of spot layout (large number of spots arranged in unit area). In ELB-Q, a large extended local background (ELB) interspot region excluding those "noise of the background" pixels is used for estimating the local background, and the quantification of spot intensities (mean and median) in the putative target spot regions is performed after further excluding background pixels in these areas based on the cutoff values established during the ELB calculation. ELB-Q takes advantage of the abundant spatial information around each spot of interest, makes no assumption of the shape and size of the spots, and needs no sophisticated adjustment. We show results of image processing using ELB-Q on both the simulated data and real DNA microarrays, which compare favorably in robustness and accuracy against those obtained with GenePix Pro 6.0 (Axon Instruments, 1999) and the Markov random field (MRF) modeling approach (O. Demirkaya et al., Bioinformatics, vol. 21, pp. 2994-3000, 2005). The ELB-Q software is developed in Matlab, and is available upon request. © 2007 IEEE.
Identifier
34548671868 (Scopus)
Publication Title
IEEE Transactions on Information Technology in Biomedicine
External Full Text Location
https://doi.org/10.1109/TITB.2006.884360
ISSN
10897771
PubMed ID
17912974
First Page
574
Last Page
582
Issue
5
Volume
11
Fund Ref
National Science Foundation
Recommended Citation
Ma, Marc Q.; Zhang, Kai; Wang, Hui Yun; and Shih, Frank Y., "ELB-Q: A new method for improving the robustness in DNA microarray image quantification" (2007). Faculty Publications. 13336.
https://digitalcommons.njit.edu/fac_pubs/13336
