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)
NoWaves0.1.zip file. Updated
29/4/09, uses better available R-package gtools instead of gregmisc.
NoWaves0.2.zip file. Updated 12/5/09, Some bugs fixed.
NoWaves0.2.tar.gz file [unix/Linux; non-tested]
NoWaves0.3.zip file. Updated 03/12/09, One bug fixed.
NoWaves0.3.tar.gz file [unix/Linux; non-tested]
NoWaves0.4.zip file. Updated 09/03/10, One bug in function SmoothNormals fixed.
NoWaves0.4.tar.gz file [unix/Linux; non-tested]
NoWaves0.6.zip 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.