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The obtained results reveal that the proposed algorithm reaches a higher level of accuracy and stability against some restrictions in microarray images such as noise, artifacts, and irregularities regarding the shapes of spots in comparison with other state-of-the-art methods.
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(i) A 'raw' zip archive contains the raw data files, i.e. the files produced by the microarray image analysis software, such as CEL files for Affymetrix GeneChips or GPR files from GenePix.
The first step is the analysis of scanned microarray images.
The segmentation of cDNA microarray spots is essential in analyzing the intensities of microarray images for biological and medical investigation.
In this paper, we propose two automated methods for analyzing microarray images.
This paper presents a Decision-Based cDNA Microarray Image filter for the removal of impulse noises for complementary deoxyribonucleic acid (cDNA) microarray images.
Microarray grid alignment and foreground separation are the basic processing steps of DNA microarray images that affect the quality of gene expression information, and hence impact our confidence in any data-derived biological conclusions.
Microarray images were analyzed using Quantarray v3.0 software (PerkinElmer).
Microarray images were acquired by GenePix 4000 microarray scanner using GenePix Pro 3 microarray analysis software (Axon Instruments, Sunnyvale, CA, USA).
Microarray slides were scanned using Agilent microarray scanner G2505B and the obtained microarray images were analyzed using the Genepix Pro™ 4.0 software.
Microarray images and quantification data were then imported into GeneTraffic DUO (Stratagene, La Jolla, CA) for analysis.
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