ArticleBioinformatics (Oxford, England)2011
aCGH.Spline--an R package for aCGH dye bias normalization.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
4 citing papers in PubMed.
- Identifying Human Genome-Wide CNV, LOH and UPD by Targeted Sequencing of Selected Regions.PloS one · 2014Article
- Large scale variation in DNA copy number in chicken breeds.BMC genomics · 2013Article
- The Growing Importance of CNVs: New Insights for Detection and Clinical Interpretation.Frontiers in genetics · 2013Article
- Characterising chromosome rearrangements: recent technical advances in molecular cytogenetics.Heredity · 2012Review
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Authors and funding
7 authors.
Funding
Abstract
motivationThe careful normalization of array-based comparative genomic hybridization (aCGH) data is of critical importance for the accurate detection of copy number changes. The difference in labelling affinity between the two fluorophores used in aCGH-usually Cy5 and Cy3-can be observed as a bias within the intensity distributions. If left unchecked, this bias is likely to skew data interpretation during downstream analysis and lead to an increased number of false discoveries.
resultsIn this study, we have developed aCGH.Spline, a natural cubic spline interpolation method followed by linear interpolation of outlier values, which is able to remove a large portion of the dye bias from large aCGH datasets in a quick and efficient manner.
conclusionsWe have shown that removing this bias and reducing the experimental noise has a strong positive impact on the ability to detect accurately both copy number variation (CNV) and copy number alterations (CNA).
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