[BioC] Normalization of Affymetrix data using the house keeping controls.

[Khan, Sohail]

Thanks Sean,

I will look at affyPLM.  However, aren't the residual plots drawn after sort of normalization has been applied?  I may be mistaken.

-Sohail

-----Original Message-----
From: Sean Davis [mailto:sdavis2 at mail.nih.gov]
Sent: Thursday, May 04, 2006 12:24 PM
To: Khan, Sohail; Bioconductor
Subject: Re: [BioC] Normalization of Affymetrix data using the house
keeping controls.





On 5/4/06 12:18 PM, "Khan, Sohail" <khan at cshl.edu> wrote:

> Dear List,
> 
> There was no response to my previous post (see below).  Is this not an
> appropriate question for this??
> 
> I have a data set from Affymetrix experiments where the assumption of "few
> changes" between control and experimental samples may not hold, so global
> normalization may be inappropriate.  I'm unsure what normalization method is
> best (house keeping genes?), etc. Thanks.

Sohail,

Unfortunately, some questions, even when appropriate will not be answered.

Will "invariant set" normalization be close to what you need?  In any case,
have you looked at affyPLM residuals, density plots, etc. to see if you can
understand how much difference there might be?

Sean