ArrayTV (version 1.10.0)

ArrayTV-package: ArrayTV-implementation of GC correction for arrays

Description

Correct gc biases in array data. The user must provide a range of windows and this function will compute the tv score for each window and correct the arrays based upon the window with the highest tv score (i.e with window showing the most gc bias)

Details

Package:

ArrayTV

Type:

Package

Version:

1.0

Date:

2012-08-02

License:

Johsn Hopkins School of Medicine

gcCorrectMain takes a matrix of array signal intensities, each column representing one array, along with vectors corresponding to probe positions and chromosomes. The gcCorrect methods enables array input for objects of class matrix, BeadStudioSet,BafLrrSet, and BafLrrSetList

References

Yuval Benjamini and Terence P. Speed. Summarizing and correcting the GC content bias in high- throughput sequencing. Nucleic Acids Res, 40(10):e72, May 2012.

Eitan Halper-Stromberg, Laurence Frelin, Ingo Ruczinski, Robert Scharpf, Chunfa Jie, Benilton Carvalho, Haiping Hao, Kurt Hetrick, Anne Jedlicka, Amanda Dziedzic, Kim Doheny, Alan F. Scott, Steve Baylin, Jonathan Pevsner, Forrest Spencer, and Rafael A. Irizarry. Performance assessment of copy number microarray platforms using a spike-in experiment. Bioinformatics, 27(8):1052

Adam B Olshen, E. S. Venkatraman, Robert Lucito, and Michael Wigler. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics, 5(4):557

See Also

type ?gcCorrectMain.Rd at the command prompt for an example