[BioC] background correction in marray

[Jake]

Hi all,

I'm working on some cDNA arrays and using maNorm() to normalize them .
In the past I've used limma to do the normalization, as it includes a
separate background-correcting function (just so I know exactly what is
happening "under the hood").  I found a posting on the list that also
noted that marray also performs some sort of background correction:

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-----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
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I've scoured the net, vignettes, etc. and have not been able to find any
conclusive information on the nature of the background correction that maNorm()
performs.  Is it just simple subtraction, ie:

maM=log2((maRf-maRb)/(maGf-maGb))

and then the maM's would be normalized via maNorm()?

Any help is much appreciated.

--Jake