Dear All, 
I am trying to normalize an affymetrix exon array. I can use
the usual normalization methods that are implemented in different packages. But
my problem is a bit different here. 
I have 4 samples, 4 affy exon microarrays. Two are treated
with let┬ say a drug. The other one is a normal array. But what I sould
mention here is that, the difference between the plus and normal sample is very
large. There will be a more than 80% difference in expression. The genes in the
plus sample will go high. My problem here I don┤ want to miss this difference,
it is very crucial for my analysis. 
When I applied the Quintile or other normalizations, the
normal samples are scaled up and I can┤ see these big differences I want to
see. The normal array is scaled up. The global normalization techniques, which
were designed with the idea that, only few genes are differentially expressed
does not work in my case.  What kind of
solution will you suggest? 
I know I can use the internal controls, but they will not
work in my case. It is a very new tech I am testing. 
Could you please suggest a good normalization method that
can remove all the systemic bias without scaling up the other array? 
With kind regards
eske



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From: "bioc-devel-request@stat.math.ethz.ch" <bioc-devel-request@stat.math.ethz.ch>
To: bioc-devel@stat.math.ethz.ch
Sent: Friday, December 19, 2008 12:00:03 PM
Subject: Bioc-devel Digest, Vol 57, Issue 3

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Today's Topics:

   1. Adding tables to an annotation package (Sean Davis)


----------------------------------------------------------------------

Message: 1
Date: Thu, 18 Dec 2008 08:17:51 -0500
From: "Sean Davis" <sdavis2@mail.nih.gov>
Subject: [Bioc-devel] Adding tables to an annotation package
To: bioC-devel <bioc-devel@stat.math.ethz.ch>,    "Marc Carlson"
    <mcarlson@fhcrc.org>
Message-ID:
    <264855a00812180517q75ab202dp4f136161565bf5db@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

Hi, Marc.

I am looking to build an annotation package with all the usual
information but will need several extra tables (still bimap, though).
Is there a suggested way to do this using AnnotationDbi/SQLForge?

Thanks,
Sean



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