Tuesday, January 16, 2018
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5.2. How to access the data from R/Bioconductor
5. Miscellaneous

A library package is provided for access to CanGEM data from the R statistical analysis environment.

It is released under the MIT license and can be downloaded from Google Code.

To install, type:
R CMD INSTALL cangem_0.1.3.tar.gz

The library contains these functions:


The first function can be used to search for microarray data from CanGEM and the second one to download that data.


The details of the analysis algorithm used to calculate gene copy numbers in CanGEM. The function cangem.preprocess downloads data from the database, performs filtering and normalization with the limma package, and combines the measurement data with the physical coordinates of the microarray probes obtained with the probe-to-genome mapping. The output of this function is then feeded to CGH Explorer.

The cangem.postprocess function reads the output of CGH Explorer, and converts the probe-based copy numbers to gene copy numbers.

2007-08-20 18:38:22 by Ilari Scheinin
2007-10-16 15:33:21 by Ilari Scheinin

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