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CSIRO Mathematics, Informatics and Statistics
CSIRO Mathematics, Informatics and Statistics
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tRMA - tools for R microarray analysisThis package contains tools for spatial median normalization and housekeeping normalization of gene microarray data. The techniques are described in the paper "New normalization methods for cDNA microarray data" are available here. The full reference for the paper is below.Some other functions for summarizing, comparing, clustering and finding differentially expressed genes are also available in tRMA. A wider range of tools is available in Bioconductor. tRMA HistorytRMA was originally written by Dale Wilson, with contributions from Scott Chapman, prior to the development of Bioconductor. In order to avoid maintenance of duplicate code and to make the routines available in a standard form the original tRMA has been converted to use Bioconductor style wherever possible. It provides wrapper functions for the convenience of the original users. The normalization routines are available in the form used by the marray packages.Installation
DocumentationThe translation to bioconductor style is still work in progress, and documentation is incomplete. The package contains a vignette, which describes use of the new normalization routines. Versions of the vignette are also available hereContactsComments, bug reports and suggestions are welcome.trma@csiro.au Reference"New normalization methods for cDNA microarray data", by D. L. Wilson, M. J. Buckley, C. A. Helliwell and I. W. Wilson, Bioinformatics vol 19, no 11 2003, pages 1325-1332 |