[BioC] limma how to ignoring background

[M PEREZ]

Hi,
I think that normalizeWithinArrays correct for background 
by default, so could be a good idea if you are going to do intrachip normalization add this
MA <- normalizeWithinArrays(RG.no.background, bg.method="none")
 
HTH
Manuel

Sean Davis <sdavis2 at mail.nih.gov> escribió:
If RG is your RGList (from read.maimages), use:


RG.no.background <- backgroundCorrect(RG,method='none')

This will take out all background values so that they will not be used 
in further analysis.

Sean

On May 5, 2005, at 11:28 AM, Guoneng Zhong wrote:

>
> Hi,
>
> My custom image result files do not have background readings. But 
> limma's
> read.maimages ask me for it. How do I get around this? I tried lying 
> to it by
> giving it some random numeric column in the result file, but am 
> worried that
> when I do normalization or lmFit it will take that fake background into
> consideration.
>
> Any advice would be appreciated.
>
> Thanks,
> g
>
> -- 
>
> Systems Programmer
> Yale Center for Medical Informatics
> fax: 203-737-5708
>
> _______________________________________________
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> Bioconductor at stat.math.ethz.ch
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