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 
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> 
> 
> 
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