[BioC] Probe level normalization

[MacDonald, James]

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]]
> >
> >
> >
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> -- 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 
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>

-- 
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