[BioC] Agilent one colour
yogi.sundaravadanam at agrf.org.au
Tue Mar 23 05:47:29 CET 2010
Thanks for this.
A bit off topic, but with two colour agilent array, I have been using just the LogRatio for downstream analysis. It makes me wonder if I should be normalising this as well.
Sorry, but I have never worked with Agilent, and FE doesn't say much.
Thanks for your help.
From: Sean Davis [mailto:seandavi at gmail.com]
Sent: Tuesday, 23 March 2010 10:38 AM
To: Yogi Sundaravadanam
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Agilent one colour
On Mon, Mar 22, 2010 at 6:23 PM, Yogi Sundaravadanam
<yogi.sundaravadanam at agrf.org.au> wrote:
> Hi all,
> I am working with Agilent one-colour array, and I find working with gProcessedSignal to be just horrible. I was just wondering if people have had experiences normalising one-colour array, and what works best.
> I was wondering if Background subtraction, followed by quantile normalisation is preferable?
gProcessedSignal is background-subtracted already, I believe, but it
is not normalized. Very rarely does the data from a one-color array
platform come normalized between arrays, a necessary step, I think.
Quantile normalization between arrays is a reasonable possibility,
yes. As with any array study, you'll want to do some quality
assessment both before and after normalization.
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