Is it possible to use the command bg.correct.gcrma in BioConductor 1.5 with R 2.1? I would like to examine the background corrected probe values using gcrma. If this command doesn't work, is there something else that will allow me to perform just the gcrma backgound correction? I found this command by searching the Bioconductor Mail archives (some correspondence about bg.correct.gcrma appeared in 2003). Even after loading affy and gcrma, I can't find any information about the command bg.correct.gcrma... > ?bg.correct.gcrma No documentation for 'bg.correct.gcrma' in specified packages and libraries: you could try 'help.search("bg.correct.gcrma")' > help.search("bg.correct.gcrma") No help files found with alias or concept or title matching 'bg.correct.gcrma' using regular expression matching.

Maybe I can include that as an option in the next release. Currently you can modify the gcrma function, at the last line, instead of return(rma(object,background=FALSE,verbose=verbose)) change it to return(object) Then you will get the object before probe level data are normalized and converted into gene level expression data. best, Jean On Thu, 5 May 2005, Ann Hess wrote: > Is it possible to use the command bg.correct.gcrma in BioConductor 1.5 > with R 2.1? I would like to examine the background corrected probe values > using gcrma. If this command doesn't work, is there something else that > will allow me to perform just the gcrma backgound correction? I found > this command by searching the Bioconductor Mail archives (some correspondence > about bg.correct.gcrma appeared in 2003). Even after loading affy > and gcrma, I can't find any information about the command bg.correct.gcrma... > > > ?bg.correct.gcrma > No documentation for 'bg.correct.gcrma' in specified packages and > libraries: > you could try 'help.search("bg.correct.gcrma")' > > help.search("bg.correct.gcrma") > No help files found with alias or concept or title matching > 'bg.correct.gcrma' using > regular expression matching. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >