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Advanced spot quality analysis in two-colour microarray experiments
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...
Autores principales: | , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2008
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2556690/ https://www.ncbi.nlm.nih.gov/pubmed/18798985 http://dx.doi.org/10.1186/1756-0500-1-80 |
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author | Yatskou, Mikalai Novikov, Eugene Vetter, Guillaume Muller, Arnaud Barillot, Emmanuel Vallar, Laurent Friederich, Evelyne |
author_facet | Yatskou, Mikalai Novikov, Eugene Vetter, Guillaume Muller, Arnaud Barillot, Emmanuel Vallar, Laurent Friederich, Evelyne |
author_sort | Yatskou, Mikalai |
collection | PubMed |
description | 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. |
format | Text |
id | pubmed-2556690 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-25566902008-10-01 Advanced spot quality analysis in two-colour microarray experiments Yatskou, Mikalai Novikov, Eugene Vetter, Guillaume Muller, Arnaud Barillot, Emmanuel Vallar, Laurent Friederich, Evelyne BMC Res Notes Short Report 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. BioMed Central 2008-09-17 /pmc/articles/PMC2556690/ /pubmed/18798985 http://dx.doi.org/10.1186/1756-0500-1-80 Text en Copyright © 2008 Friederich et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Short Report Yatskou, Mikalai Novikov, Eugene Vetter, Guillaume Muller, Arnaud Barillot, Emmanuel Vallar, Laurent Friederich, Evelyne Advanced spot quality analysis in two-colour microarray experiments |
title | Advanced spot quality analysis in two-colour microarray experiments |
title_full | Advanced spot quality analysis in two-colour microarray experiments |
title_fullStr | Advanced spot quality analysis in two-colour microarray experiments |
title_full_unstemmed | Advanced spot quality analysis in two-colour microarray experiments |
title_short | Advanced spot quality analysis in two-colour microarray experiments |
title_sort | advanced spot quality analysis in two-colour microarray experiments |
topic | Short Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2556690/ https://www.ncbi.nlm.nih.gov/pubmed/18798985 http://dx.doi.org/10.1186/1756-0500-1-80 |
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