Hello, I am new to Bioconductor. I have read four of my .gpr files using the read.GenePix() method of marray package. Now I want to subtract the background from foreground of the Cy5 values and calculate the global median normalization on the subtracted values. I don't know how to find the subtracted values for Cy5 values. Any help is greatly appreciated. If you could show how this could be done using swirl dataset, that will be great. I tried RGsubbed<-backgroundCorrect(dat.scat.cy5, method = BGsubmethod, verbose = FALSE) but I am getting Error in backgroundCorrect(dat.scat.cy5, method = BGsubmethod, verbose = FALSE) : object 'BGsubmethod' not found I have loaded marray and limma libraries. dat.scat.cy5 is my marray object where I read the .gpr files. Thanks -- output of sessionInfo(): > RGsubbed<-backgroundCorrect(dat.scat.cy5, method = BGsubmethod, verbose = FALSE) Error in backgroundCorrect(dat.scat.cy5, method = BGsubmethod, verbose = FALSE) : object 'BGsubmethod' not found -- Sent via the guest posting facility at bioconductor.org.

Hi John, On 7/28/2013 2:48 PM, John Velu [guest] wrote: > Hello, > > I am new to Bioconductor. I have read four of my .gpr files using the read.GenePix() method of marray package. Now I want to subtract the background from foreground of the Cy5 values and calculate the global median normalization on the subtracted values. I don't know how to find the subtracted values for Cy5 values. Any help is greatly appreciated. If you could show how this could be done using swirl dataset, that will be great. > > I tried RGsubbed<-backgroundCorrect(dat.scat.cy5, method = BGsubmethod, verbose = FALSE) but I am getting Error in backgroundCorrect(dat.scat.cy5, method = BGsubmethod, verbose = FALSE) : > object 'BGsubmethod' not found The method argument takes a character string, not an object (e.g., in R, BGsubmethod is an object, and "BGsubmethod" is character). Best, Jim > I have loaded marray and limma libraries. dat.scat.cy5 is my marray object where I read the .gpr files. > > Thanks > > -- output of sessionInfo(): > >> RGsubbed<-backgroundCorrect(dat.scat.cy5, method = BGsubmethod, verbose = FALSE) > Error in backgroundCorrect(dat.scat.cy5, method = BGsubmethod, verbose = FALSE) : > object 'BGsubmethod' not found > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099