Introduction

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.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.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).

Publications

  1. aCGH.Spline--an R package for aCGH dye bias normalization.
    Cite this
    Fitzgerald TW, Larcombe LD, Le Scouarnec S, Clayton S, Rajan D, Carter NP, Redon R, 2011-05-01 - Bioinformatics (Oxford, England)

Credits

  1. Tomas W Fitzgerald
    Developer

    Wellcome Trust Sanger Institute, Hinxton, Germany

  2. Lee D Larcombe
    Developer

  3. Solena Le Scouarnec
    Developer

  4. Stephen Clayton
    Developer

  5. Diana Rajan
    Developer

  6. Nigel P Carter
    Developer

  7. Richard Redon
    Investigator

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Summary
AccessionBT001512
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Submitted ByRichard Redon