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 associations. 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