R help - Jul 2012 - R bioconductor agilent aCGH analysis

Hi,

I would like to analyze some agilent aCGH copy number files. As a start, I
would like to normalize this data. I don't know what is the standard way to
do this. Which package is the standard one that people use for this
purpose? The chips that I am looking at are the agilent sure print 1M
(G4447a) array and a custom chip with similar format. My raw data is a text
file with spot locations and intensities. It is a two color array.

Thanks for your help!

	[[alternative HTML version deleted]]

HI,

I think you will get better response if you post in bioconductor mailing list
(http://www.bioconductor.org/help/mailing-list/).

A.K.



----- Original Message -----
From: Preeti <preeti at sci.utah.edu>
To: r-help at r-project.org
Cc: 
Sent: Friday, July 27, 2012 6:05 PM
Subject: [R] R bioconductor agilent aCGH analysis

Hi,

I would like to analyze some agilent aCGH copy number files. As a start, I
would like to normalize this data. I don't know what is the standard way to
do this. Which package is the standard one that people use for this
purpose? The chips that I am looking at are the agilent sure print 1M
(G4447a) array and a custom chip with similar format. My raw data is a text
file with spot locations and intensities. It is a two color array.

Thanks for your help!

??? [[alternative HTML version deleted]]

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On Jul 27, 2012, at 3:05 PM, Preeti wrote:
> Hi,
>
> I would like to analyze some agilent aCGH copy number files. As a  
> start, I
> would like to normalize this data. I don't know what is the standard  
> way to
> do this. Which package is the standard one that people use for this
> purpose? The chips that I am looking at are the agilent sure print 1M
> (G4447a) array and a custom chip with similar format. My raw data is  
> a text
> file with spot locations and intensities. It is a two color array.
http://www.bioconductor.org/help/mailing-list/
> Thanks for your help!
>
> 	[[alternative HTML version deleted]]
http://www.bioconductor.org/help/mailing-list/posting-guide
>
-- 

David Winsemius, MD