Hi, Is there a way to access the "background" intensity used in the gcrma or rma algorithm of the affy package? For example, after running gcrma() can I get the background for all the chips in the exprSet? Thanks for your advice. Sohail Khan Scientific Programmer COLD SPRING HARBOR LABORATORY Genome Research Center 500 Sunnyside Boulevard Woodbury, NY 11797 (516)422-4076

GCRMA and RMA do not estimate "background intensity", but rather some parameters for the distribution(s) of background intensity. The internal functions bg.parameters(for rma) and bg.parameters.ns (for gcrma) estimate those but you need to read the related papers to see what the parameters are. And notice the distributional assumptions are different in rma and gcrma. Jean On Fri, 31 Mar 2006, Khan, Sohail wrote: > Hi, > > Is there a way to access the "background" intensity used in the gcrma or rma algorithm of the affy package? For example, after running gcrma() can I get the background for all the chips in the exprSet? Thanks for your advice. > > > Sohail Khan > Scientific Programmer > COLD SPRING HARBOR LABORATORY > Genome Research Center > 500 Sunnyside Boulevard > Woodbury, NY 11797 > (516)422-4076 > > _______________________________________________ > 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 >

Thank you Jean. Could you point me to the references? -Sohail -----Original Message----- From: Zhijin (Jean) Wu [mailto:zwu@alexander.stat.brown.edu] Sent: Friday, March 31, 2006 11:42 AM To: Khan, Sohail Cc: Bioconductor at stat.math.ethz.ch Subject: Re: [BioC] GCRMA-Background GCRMA and RMA do not estimate "background intensity", but rather some parameters for the distribution(s) of background intensity. The internal functions bg.parameters(for rma) and bg.parameters.ns (for gcrma) estimate those but you need to read the related papers to see what the parameters are. And notice the distributional assumptions are different in rma and gcrma. Jean On Fri, 31 Mar 2006, Khan, Sohail wrote: > Hi, > > Is there a way to access the "background" intensity used in the gcrma or rma algorithm of the affy package? For example, after running gcrma() can I get the background for all the chips in the exprSet? Thanks for your advice. > > > Sohail Khan > Scientific Programmer > COLD SPRING HARBOR LABORATORY > Genome Research Center > 500 Sunnyside Boulevard > Woodbury, NY 11797 > (516)422-4076 > > _______________________________________________ > 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 >