[BioC] background correction with cDNA array data

[David Ruau]

You can also have a look at the recent book: "Bioinformatics and 
Computational Biology Solutions Using R and Bioconductor"
from Robert Gentleman, Vince Carey, Wolfgang Huber, Rafael Irizarry and 
Sandrine Dudoit.
http://www.bioconductor.org/pub/docs/mogr/
They have done a great job.

David

On Oct 27, 2005, at 5:01, Qi.Zhang at astrazeneca.com wrote:

> 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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>
> Naomi S. Altman                                814-865-3791 (voice)
> Associate Professor
> Dept. of Statistics                              814-863-7114 (fax)
> Penn State University                         814-865-1348 (Statistics)
> University Park, PA 16802-2111
>
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