cleancdf <- cleancdfname(rawdata at cdfName,addcdf=FALSE) : I copied this command from the actual code in case anybody refer that code (https://stat.ethz.ch/pipermail/bioconductor/2006-September/01424 2.html). Now be happy as I have sorted out the problem. So, your time is save now. Thanks anyway, Farhat ________________________________________ From: James W. MacDonald [jmacdon@med.umich.edu] Sent: 14 January 2010 18:27 To: Memon, Farhat N Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] help needed for GCRMA Memon, Farhat N wrote: > Thanks Jim. > > I am getting error while using the following step: > cleancdf <- cleancdfname(rawdata at cdfName,addcdf=FALSE) Is that really the code you are using? If so, please note that you can't pass a variable name with spaces to _any_ R function, so something like that will never work. Also, what you have given here isn't enough information to give you an answer. I suppose I could go dig up the function you are using and try to figure out what went wrong, but that is a lot of work for me to do for you (for free). In the future, remember that most of the people who answer questions on this or any listserv are busy, so your best bet is to make it easy for them to answer your question. Some hints for how to do that can be found in the posting guide: http://www.bioconductor.org/docs/postingGuide.html as well as the R-help posting guide http://www.r-project.org/posting-guide.html I can hazard a guess that what you really want is something like cleancdf <- cleancdfname(rawdata at cdfName, addcdf = FALSE) I would also hazard a guess that the 'rawdata at cdfName' isn't really what you want there, unless your AffyBatch is really called 'rawdata'. Instead you should substitute the real AffyBatch variable name. Best, Jim > > Any suggestion........please. > > Regards, > Farhat > ________________________________________ > From: James W. MacDonald [jmacdon at med.umich.edu] > Sent: 14 January 2010 16:32 > To: Memon, Farhat N > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] help needed for GCRMA > > Hi Farhat, > > Memon, Farhat N wrote: >> Hi, >> >> I am a new user of GCRMA package. I want to use GCRMA method to calculate expression values of some probeset for which I used the following code: >> >> library(gcrma) >> library(affy) >> data=ReadAffy() >> gcrma.set=gcrma(data) >> gcrma.exp=exprs(gcrma.set) >> >> According to my understand, this code will calculate the expression values of all the probesets. Now, I want to calculate the expression values of probesets excluding some of their probes. >> > > See the following post: > > https://stat.ethz.ch/pipermail/bioconductor/2006-September/014242.html > > Best, > > Jim > > >> If anyone can help >> >> Regards >> Farhat >> _______________________________________________ >> 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 > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues > -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues