Smoothing waves in aCGH tumor profiles

This site corresponds to the paper:

Mark A van de Wiel, Rebecca Brosens, Paul HC Eilers, Candy Kumps, Gerrit A Meijer, Björn Menten, Erik Sistermans, Frank Speleman, Marieke E Timmerman and Bauke Ylstra (2009) Smoothing waves in array CGH tumor profiles.
Bioinformatics. 25, 1099-1104.

The R-package (replaces the earlier R-scripts) file. Updated 29/4/09, uses better available R-package gtools instead of gregmisc.  file. Updated 12/5/09, Some bugs fixed.
NoWaves0.2.tar.gz file [unix/Linux; non-tested]  file. Updated 03/12/09, One bug fixed. 
NoWaves0.3.tar.gz file [unix/Linux; non-tested]  file. Updated 09/03/10, One bug in function SmoothNormals fixed. 
NoWaves0.4.tar.gz file [unix/Linux; non-tested]  file. Updated 17/04/15, Compiled under R>=3.0.0
NoWaves0.6.tar.gz file [unix/Linux; non-tested]
Example file on how to use the package

Additional input data sets (package contains small example data sets)

Dutch Zip-file, containing two .Rdata Agilent 44K data sets corresponding to 5 tumor profiles and
29 clinical genetics profiles. Matched data sets.
Belgian Zip-file, containing three .txt Agilent 44K data sets corresponding to 20 tumor profiles, 20 clinical genetics profiles and 20 artificial tumor profiles (see article). Matched data sets. Extensive coverage of chromosome 17.
Agilent 105K calibration set (.Rdata). Contains 26 calibration profiles from clinical genetics.
Agilent 180K calibration set (.Rdata). Contains 16 calibration profiles from clinical genetics.
NimbleGen135K calibration set (.Rdata). Contains 49 calibration profiles. May also be used for dewaving higher resolution tumor profiles.

Output plots

Plots Dutch profiles, containing 5 segmented uncorrected and corrected profile plots
Plots Belgian profiles, containing 20 segmented uncorrected and corrected profile plots
Plots artificial tumor profiles, containing 20 segmented uncorrected and corrected artificial tumor profile plots. These profiles are created by adding aberrations to normal profiles. Each plot consists of three parts: the original (normal) profile, the uncorrected artificial profile and the corrected artificial profile. Green areas indicate the locations of the artificial aberrations.

Other platforms

Calibration profiles from the commercial Affymetrix 500K SNP platform are available from GEO, accession number GSE5173. Note that GEO profiles may be imported in R by using the package GEOquery, available from Bioconductor.

Calibration profiles from the The Wellcome Trust Sanger Institute WGTP (Whole Genome Tiling Path) platform are available from ArrayExpress, accession number E-TABM-107.