I am using the affy library to compute RMA values on mouse exon arrays, using the mouseexonpmcdf from here: http://xmap.picr.man.ac.uk/download#mmcdf It works fine, but I wanted to check some of the details of the implementation and hoped somebody on this list could help. As I understand it, the background correction step of the RMA calculation usually works on the mismatch (MM) probes on the array. However, on the exon array, there are no MM probes, so the calculation is done based on a separate pool of background probes. There is a description here: http://media.affymetrix.com/support/technical/whitepapers/exon_backgro und_correction_whitepaper.pdf Is this seamlessly happening behind the scenes when I run RMA with the mouse exon CDF or do I need to do something else to ensure the proper background correction is taking place? Peter

Peter, the beauty of RMA is its independency on the MM probes. The bg correction on the whitepaper you point to is not the one used by RMA. Assuming that the PMs measure background + signal, given some distributional properties (background is normal; signal is exponential), what the background correction step in RMA does is to estimate the signal conditional on the fact that you observed signal+background: S ~ Normal() B ~ Exponential() E[S | B+S] cheers, b On 24 November 2010 13:27, Peter Saffrey <pzs at="" dcs.gla.ac.uk=""> wrote: > I am using the affy library to compute RMA values on mouse exon arrays, > using the mouseexonpmcdf from here: > > http://xmap.picr.man.ac.uk/download#mmcdf > > It works fine, but I wanted to check some of the details of the > implementation and hoped somebody on this list could help. > > As I understand it, the background correction step of the RMA calculation > usually works on the mismatch (MM) probes on the array. However, on the exon > array, there are no MM probes, so the calculation is done based on a > separate pool of background probes. There is a description here: > > http://media.affymetrix.com/support/technical/whitepapers/exon_backg round_correction_whitepaper.pdf > > Is this seamlessly happening behind the scenes when I run RMA with the mouse > exon CDF or do I need to do something else to ensure the proper background > correction is taking place? > > Peter > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >