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CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data.

Bollen S, Leddin M, Andrade-Navarro MA, Mah N - Bioinformatics (2014)

Bottom Line: 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.CAFE will also be freely available from Bioconductor. sander.h.bollen@gmail.com or nancy.mah@mdc-berlin.de Supplementary data are available at Bioinformatics online.

View Article: PubMed Central - PubMed

Affiliation: 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.

ABSTRACT

Summary: 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.

Availability and implementation: 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.

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

Supplementary information: Supplementary data are available at Bioinformatics online.

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Related in: MedlinePlus

Samples GSM652238 (orange) and GSM652239 (blue) from GEO dataset GSE26526 were plotted. GSM652238 is known to have a deletion in Chromosome 11q. (A) The output of slidPlot(). (B) The output of discontPlot()
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btu028-F1: Samples GSM652238 (orange) and GSM652239 (blue) from GEO dataset GSE26526 were plotted. GSM652238 is known to have a deletion in Chromosome 11q. (A) The output of slidPlot(). (B) The output of discontPlot()

Mentions: For all plot functions except facetPlot(), it is possible to add a chromosome idiogram over the chromosome plot. This allows easy visualization of chromosomal abnormalities. See Figure 1 for example plots. All plots are printed to the file system and returned as ggplot2 objects. Plot parameters, such as labels and scales, can be modified to the user's liking by altering the ggplot2 object.Fig. 1.


CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data.

Bollen S, Leddin M, Andrade-Navarro MA, Mah N - Bioinformatics (2014)

Samples GSM652238 (orange) and GSM652239 (blue) from GEO dataset GSE26526 were plotted. GSM652238 is known to have a deletion in Chromosome 11q. (A) The output of slidPlot(). (B) The output of discontPlot()
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4016701&req=5

btu028-F1: Samples GSM652238 (orange) and GSM652239 (blue) from GEO dataset GSE26526 were plotted. GSM652238 is known to have a deletion in Chromosome 11q. (A) The output of slidPlot(). (B) The output of discontPlot()
Mentions: For all plot functions except facetPlot(), it is possible to add a chromosome idiogram over the chromosome plot. This allows easy visualization of chromosomal abnormalities. See Figure 1 for example plots. All plots are printed to the file system and returned as ggplot2 objects. Plot parameters, such as labels and scales, can be modified to the user's liking by altering the ggplot2 object.Fig. 1.

Bottom Line: 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.CAFE will also be freely available from Bioconductor. sander.h.bollen@gmail.com or nancy.mah@mdc-berlin.de Supplementary data are available at Bioinformatics online.

View Article: PubMed Central - PubMed

Affiliation: 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.

ABSTRACT

Summary: 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.

Availability and implementation: 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.

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

Supplementary information: Supplementary data are available at Bioinformatics online.

Show MeSH
Related in: MedlinePlus