[BioC] Agilent one colour

[Sean Davis]

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