[BioC] background correction with cDNA array data

[Qi.Zhang@astrazeneca.com]

Naomi, thanks for your reply.  I do not intent to write my own mathod.  I
took the default option when read in the gpr file using read.GenePix, so I
assume the background correction was done by "substraction".  I remember it
from somewhere that the "substraction" may introduce additional variance
depends on the algorithm of the background estimation (from the iamge
analysis software).  Is the "substraction" the only bg correction method in
marray?  limma has more options, but I have no idea about the advantage or
disadvantage of them.  Any suggestions will be very helpful.

Thanks.

Qi

-----Original Message-----
From: Naomi Altman [mailto:naomi at stat.psu.edu]
Sent: Wednesday, October 26, 2005 7:42 PM
To: Zhang, Qi; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] background correction with cDNA array data


Did you want to write your own background correction method?  The 
normalization routines in marray and limma do background correction.

--Naomi

At 04:51 PM 10/26/2005, Qi.Zhang at astrazeneca.com wrote:
>Dear all,
>
>I have searched through the bioconductor ducument and this mailing list,
but
>could not find a general guidance about how to correct background in cDNA
>array data.  I have imported my data (GPR files from GenePix) using
>functions from marray.  Now what are the available methods for background
>correction before normalization?  Any suggestions/experience is very much
>appreciated.
>
>Regards,
>
>Qi Zhang
>
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>Bioconductor at stat.math.ethz.ch
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
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