Hi all, How can I retrieve raw expression dataset from CEL files? I don't want normalized dataset...I have already read the CELL files using the following statements: library(gcrma) Data <- ReadAffy("file1.CEL") what would be my next steps? Thanks in advance, Anirban [[alternative HTML version deleted]]

Hi Anirban, Please define 'retrieve'. When you read the data into an AffyBatch using ReadAffy, you then have the raw expression dataset. What exactly do you want to do with it? Best, Jim On 9/14/2011 6:21 AM, ANIRBAN BHAR wrote: > Hi all, > > How can I retrieve raw expression dataset from CEL files? I don't want > normalized dataset...I have already read the CELL files using the following > statements: > > > library(gcrma) > Data<- ReadAffy("file1.CEL") > > > what would be my next steps? > > Thanks in advance, > > Anirban > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 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

Hi Anirban, Please don't take things off-list. We like to think the list archives will be useful for people to search. On 9/14/2011 9:44 AM, ANIRBAN BHAR wrote: > Hi James, > > Thanks for your reply.. I want to have expression matrix from CEL > file. My question is : do I need to use rma() or some other method to > get the matrix? You still need to clarify what you want, as this question doesn't mesh with your previous question. By definition the results from rma() will not be 'raw' expression data, but will have been processed by rma(). So please explain *exactly* what you want. What do you mean by 'get' the matrix? What do you mean by 'raw' expression data? What do you mean by 'expression matrix'? What exactly are you trying to do? Note that I'm not trying to be difficult here. Depending on what I assume you mean, I could come up with multiple answers to your questions. If you want to get the right answer, you have to ask the question in a manner that removes any need to interpret what you are getting at. Best, Jim > > Best regards, > > Anirban > > On Wed, Sep 14, 2011 at 3:18 PM, James W. MacDonald > <jmacdon@med.umich.edu <mailto:jmacdon@med.umich.edu="">> wrote: > > Hi Anirban, > > Please define 'retrieve'. When you read the data into an AffyBatch > using ReadAffy, you then have the raw expression dataset. What > exactly do you want to do with it? > > Best, > > Jim > > > > > On 9/14/2011 6:21 AM, ANIRBAN BHAR wrote: > > Hi all, > > How can I retrieve raw expression dataset from CEL files? I > don't want > normalized dataset...I have already read the CELL files using > the following > statements: > > > library(gcrma) > Data<- ReadAffy("file1.CEL") > > > what would be my next steps? > > Thanks in advance, > > Anirban > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org <mailto:bioconductor@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 > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 <tel: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 [[alternative HTML version deleted]]