RefPlus: an R package extending the RMA Algorithm.

UNLABELLED: RMA has become a widely used methodology to pre-process Affymetrix gene expression microarrays. A limitation of RMA is that the calculated probeset intensities change when a set of microarrays is re-pre-processed after the inclusion of additional microarrays into the analysis set. Here we report the availability of the RefPlus package containing functions to perform the Extrapolation Strategy and Extrapolation Averaging algorithms which address these issues. AVAILABILITY: The software is implemented in the R language and can be downloaded from the Bioconductor project website (http://www.bioconductor.org). SUPPLEMENTARY INFORMATION: Further details of the workings and evaluation of these functions are given in the documentation available on the Bioconductor website.