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?
Best,
Yogi
[[alternative HTML version deleted]]
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
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@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
On Tue, Mar 23, 2010 at 12:47 AM, Yogi Sundaravadanam
<yogi.sundaravadanam at="" agrf.org.au=""> wrote:
> 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.
>
Hi, Yogi. You might need to look into some background on microarray
data analysis. Generally, if you want to compare between microarray
experiments, you'll want to do a significant amount of quality control
and assessment to be sure and I think most people would agree that
normalization usually improves downstream inference. In other words,
QA/QC and normalization are probably necessary steps in microarray
data analysis.
> Sorry, but I have never worked with Agilent, and FE doesn't say
much.
The Agilent FE manual does not lay out an analysis recipe, I agree.
However, it is useful for determining what data are represented in the
FE .txt file. I would recommend having it handy when analyzing
Agilent data, in any case.
Sean
> -----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
>
