Hi, I am using affymetrix platform for expression analysis. I need to perform  the normalization of each of  individual probes intensities which belong to a probeset (without the summarization of individual probe intensities of a probeset). Further I would like to perform statistical analysis on the normalized intensities of the individual probes to identify those probes that are significantly regulated between different conditions or treatments. How to perform the normalization using the individual probe expression values instead of the probeset expression values in Limma or any other bioconductor package?? Thank you in advance.. Regrads, Suresh V. ________________________________ From: James W. MacDonald <jmacdon@med.umich.edu> Cc: "bioconductor@r-project.org" <bioconductor@r-project.org> Sent: Wednesday, November 30, 2011 4:00 PM Subject: Re: [BioC] Probe level normalization Hi Suresh, On 11/30/2011 7:49 AM, suri ghani wrote: > How to perform the normalization using the individual probe expression values instead of the probeset expression values in Limma or any other bioconductor package?? I'm not sure what you are asking here. Could you please rephrase? What platform are you talking about here? The term 'probeset' usually pertains to the Affymetrix microarray platform. If you are in fact using Affy data, then you won't use limma for normalization. If you state clearly what you are trying to do, then maybe someone can help. Best, Jim > > Thanks in advance.. > > Regards, Suresh >     [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > 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 ********************************************************** 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]]

Hi Suresh, Hypothetically you could do something like dat <- ReadAffy() dat <- bg.correct(dat, "rma") dat <- normalize(dat, method = "quantiles") Which will give you the normalized, background corrected probes. I doubt limma will take an AffyBatch as input, so you would have to extract the probes using the exprs() extractor. Alternatively, you could use the affyPLM package, which stands for affy Probe Level Model. You can specify different probe level models - see the vignette for more information. Best, Jim On 11/30/11 6:19 PM, suri ghani wrote: > Hi, > > I am using affymetrix platform for expression analysis. > I need to perform the normalization of each of individual probes > intensities which belong to a probeset (without the summarization of > individual probe intensities of a probeset). Further I would like to > perform statistical analysis on the normalized intensities of the > individual probes to identify those probes that are significantly > regulated between different conditions or treatments. > How to perform the normalization using the individual probe expression > values instead of the probeset expression values in Limma or any other > bioconductor package?? > > Thank you in advance.. > > Regrads, > Suresh V. > > -------------------------------------------------------------------- ---- > *From:* James W. MacDonald <jmacdon at="" med.umich.edu=""> > *To:* suri ghani <suri_ghani at="" yahoo.com=""> > *Cc:* "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> > *Sent:* Wednesday, November 30, 2011 4:00 PM > *Subject:* Re: [BioC] Probe level normalization > > Hi Suresh, > > On 11/30/2011 7:49 AM, suri ghani wrote: > > How to perform the normalization using the individual probe > expression values instead of the probeset expression values in Limma > or any other bioconductor package?? > > I'm not sure what you are asking here. Could you please rephrase? What > platform are you talking about here? > > The term 'probeset' usually pertains to the Affymetrix microarray > platform. If you are in fact using Affy data, then you won't use limma > for normalization. > > If you state clearly what you are trying to do, then maybe someone can > help. > > Best, > > Jim > > > > > > Thanks in advance.. > > > > Regards, Suresh > > [[alternative HTML version deleted]] > > > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org <mailto: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 > > -- 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