ACGH.Spline--an R package for aCGH dye bias normalization.
Ontology highlight
ABSTRACT: Motivation
The 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.Results
In 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.Conclusions
We 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).
SUBMITTER: Fitzgerald TW
PROVIDER: S-EPMC3077069 | biostudies-literature | 2011 May
REPOSITORIES: biostudies-literature
Publications
aCGH.Spline--an R package for aCGH dye bias normalization.
Fitzgerald Tomas W TW Larcombe Lee D LD Le Scouarnec Solena S Clayton Stephen S Rajan Diana D Carter Nigel P NP Redon Richard R
Bioinformatics (Oxford, England) 20110225 9
<h4>Motivation</h4>The 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.<h4>Resul ...[more]
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