[BioC] SIM new package for Statistical Integration of Microarrays

Maarten van Iterson M.van_iterson.HG at lumc.nl
Tue Sep 16 16:28:12 CEST 2008

dear all, 

The Statistical Integration of Microarrays (SIM) package implements
methods to simultaneously analyze DNA copy number and RNA expression
microarray data, as described in Menezes et al. We propose the use of a
random-effects model to fit the association between copy number and gene
expression microarray data, measured on the same samples but not
necessarily using the same array platform. It makes use of gene sets
rather than individual genes to improve power of detection of subtle

The model (and this package) can be applied to either intensity or ratio
data. Moreover, it can be used to describe the association between any
other two microarray data sources, such as methylation and expression,
or SNP call and expression, for example. Our approach has several
advantages over existing methods, including the use of either continuous
of user-discretized copy number data. Also, our model allows for using
confounder variables, such as clinical variables, and does not require
mapping between copy number and expression probes. The package includes
many tools for visualization. A limited number of those is already
available on the current devel version, with many under current testing
which will be incorporated shortly.

The current version of the package is particularly suited to analyze
data with copy number changes spanning larger regions, such as those
from cancer samples. Future extensions will include settings better
suited for investigating the effects of changes spanning smaller
regions, such as in natural copy number variation.

Ref: Menezes RX, Boetzer M, Sieswerda M, van Ommen GJB, Boer JM.
Integrated statistical analysis to identify associations between DNA
copy number and gene expression in microarray data (submitted 2008).

Maarten van Iterson
Center for Human and Clinical Genetics
Leiden University Medical Center (LUMC)
Research Building, Einthovenweg 20 
Room S-04-005
Phone: 071-526 9428
E-mail: M.van_iterson.HG at lumc.nl
Postal address:
Postzone S-04-P
Postbus 9600
2300 RC Leiden 
The Netherlands

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