[BioC] Loess normalization for Agilent chips

Malard, Joel M JM.Malard at pnl.gov
Fri Sep 17 23:32:03 CEST 2004


Thank you for pointing this out.
 
I had not seen that read.maimages() can process 'agilent' files and
thought all the data structures had to be filled in manually.

Best wishes,

Joel

-----Original Message-----
From: A.J. Rossini [mailto:rossini at blindglobe.net] 
Sent: Friday, September 17, 2004 12:53 PM
To: Malard, Joel M
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Loess normalization for Agilent chips



Why not just use Limma and the corresponding tools?

It's FAR easier that way.   That way you actually get what you pay
for, rather than far less...



"Malard, Joel M" <JM.Malard at pnl.gov> writes:

> I am struggling to get data from Agilent cDNA arrays into 
> BioConductor. It seems to me much easier to get the data in affy's 
> normalize.loess() than in the other cDNA array packages.
>
> Given that "one who get a bargain get what he pays for", does anyone 
> has comments, recommendations or warnings to share about using an Affy

> normalization procedure on cDNA data?
>
> Thanks,
>
> Joel M. Malard, Ph.D.
> Scientist IV
> Pacific Northwest National Laboratory
> Battelle Boulevard, PO Box 999
> Mail Stop K1-85
> Richland, WA 99352
>
> "I love the audacity of those who have everything to loose from it; 
> the moderation of those who have nothing to gain from it." Rostand, 
> Jean
> (1894-1977)
>
>
>
> 	[[alternative HTML version deleted]]
>
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-- 
Anthony Rossini			    Research Associate Professor
rossini at u.washington.edu            http://www.analytics.washington.edu/

Biomedical and Health Informatics   University of Washington
Biostatistics, SCHARP/HVTN          Fred Hutchinson Cancer Research
Center
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