CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data.
CONCLUSIONS
The current methods available to detect chromosomal abnormalities from DNA microarray expression data are cumbersome and inflexible. CAFE has been developed to alleviate these issues. It is implemented as an R package that analyzes Affymetrix *.CEL files and comes with flexible plotting functions, easing visualization of chromosomal abnormalities.


METHODS
CAFE is available from https://bitbucket.org/cob87icW6z/cafe/ as both source and compiled packages for Linux and Windows. It is released under the GPL version 3 license. CAFE will also be freely available from Bioconductor.


BACKGROUND
sander.h.bollen@gmail.com or nancy.mah@mdc-berlin.de


BACKGROUND
Supplementary data are available at Bioinformatics online.
Computational Biology and Data Mining Group, Max Delbruck Center for Molecular Medicine, 13125 Berlin, Germany, Graduate School of Life Sciences, Utrecht University, Universiteitsweg 98, 3584 CG, Utrecht, the Netherlands and Roche Diagnostics GmbH, 82377 Penzberg, Germany.
Sander
S
Bollen
Mathias
M
Leddin
Miguel A
MA
Andrade-Navarro
Nancy
N
Mah
D002869:Chromosome Aberrations; D015870:Gene Expression; D008390:Markov Chains; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012984:Software