[BioC] GCRMA-Background

[Khan, Sohail]

Thank you Jean.
Could you point me to the references?

-Sohail

-----Original Message-----
From: Zhijin (Jean) Wu [mailto:zwu at alexander.stat.brown.edu]
Sent: Friday, March 31, 2006 11:42 AM
To: Khan, Sohail
Cc: Bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] GCRMA-Background


GCRMA and RMA do not estimate "background intensity", but rather some
parameters for the distribution(s) of  background intensity. The internal
functions bg.parameters(for rma) and bg.parameters.ns (for gcrma) estimate
those but you need to read the related papers to see what the parameters
are. And notice the distributional assumptions are different in rma and
gcrma.

Jean
On Fri, 31 Mar 2006, Khan, Sohail wrote:

> Hi,
>
> Is there a way to access the "background" intensity used in the gcrma or rma algorithm of the affy package? For example, after running gcrma() can I get the background for all the chips in the exprSet?  Thanks for your advice.
>
>
> Sohail Khan
> Scientific Programmer
> COLD SPRING HARBOR LABORATORY
> Genome Research Center
> 500 Sunnyside Boulevard
> Woodbury, NY 11797
> (516)422-4076
>
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