Reference : Advanced spot quality analysis in two-colour microarray experiments
Scientific journals : Article
Life sciences : Biochemistry, biophysics & molecular biology
http://hdl.handle.net/10993/6271
Advanced spot quality analysis in two-colour microarray experiments
English
Yatskou, M. [Microarray Center, LBMAGM, CRP-Santé, 84 Rue Val Fleuri, L-1526, Luxembourg, Luxembourg ; University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Life Science Research Unit > Cytoskeleton and Cell Plasticity Laboratory]
Novikov, E. [Institut Curie, Service Bioinformatique, Institute Curie, 26 Rue d'Ulm, Paris, F-75248, France, INSERM, U900, Paris, F-75248, France, Ecole des Mines de Paris, Fontainebleau, F-77300, France]
Vetter, G. [Microarray Center, LBMAGM, CRP-Santé, 84 Rue Val Fleuri, L-1526, Luxembourg, Luxembourg ; University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Life Science Research Unit > Cytoskeleton and Cell Plasticity Laboratory]
Muller, A. [Microarray Center, LBMAGM, CRP-Santé, 84 Rue Val Fleuri, L-1526, Luxembourg, Luxembourg]
Barillot, E. [Institut Curie, Service Bioinformatique, Institute Curie, 26 Rue d'Ulm, Paris, F-75248, France, INSERM, U900, Paris, F-75248, France, Ecole des Mines de Paris, Fontainebleau, F-77300, France]
Vallar, L. [Microarray Center, LBMAGM, CRP-Santé, 84 Rue Val Fleuri, L-1526, Luxembourg, Luxembourg]
Friederich, Evelyne mailto [University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Life Science Research Unit >]
2008
BMC Research Notes
Biomed Central
1
Yes (verified by ORBilu)
International
1756-0500
[en] Background: Image analysis of microarrays and, in particular, spot quantification and spot quality control, is one of the most important steps in statistical analysis of microarray data. Recent methods of spot quality control are still in early age of development, often leading to underestimation of true positive microarray features and, consequently, to loss of important biological information. Therefore, improving and standardizing the statistical approaches of spot quality control are essential to facilitate the overall analysis of microarray data and subsequent extraction of biological information. Findings: We evaluated the performance of two image analysis packages MAIA and GenePix (GP) using two complementary experimental approaches with a focus on the statistical analysis of spot quality factors. First, we developed control microarrays with a priori known fluorescence ratios to verify the accuracy and precision of the ratio estimation of signal intensities. Next, we developed advanced semi-automatic protocols of spot quality evaluation in MAIA and GP and compared their performance with available facilities of spot quantitative filtering in GP. We evaluated these algorithms for standardised spot quality analysis in a whole-genome microarray experiment assessing well-characterised transcriptional modifications induced by the transcription regulator SNAI1. Using a set of RT-PCR or qRT-PCR validated microarray data, we found that the semi-automatic protocol of spot quality control we developed with MAIA allowed recovering approximately 13% more spots and 38% more differentially expressed genes (at FDR = 5%) than GP with default spot filtering conditions. Conclusion: Careful control of spot quality characteristics with advanced spot quality evaluation can significantly increase the amount of confident and accurate data resulting in more meaningful biological conclusions. © 2008 Friederich et al; licensee BioMed Central Ltd.
http://hdl.handle.net/10993/6271
10.1186/1756-0500-1-80

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