ACGH.Spline--an R package for aCGH dye bias normalization.

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

SUBMITTER: Fitzgerald TW 

PROVIDER: S-EPMC3077069 | biostudies-literature | 2011 May

REPOSITORIES: biostudies-literature