[BioC] Agilent one colour

[Yogi Sundaravadanam]

Hi Sean,

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.

Best,
Yogi 

-----Original Message-----
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?

Hi, Yogi.

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.

Sean