[BioC] limma how to ignoring background

[Guoneng Zhong]

So based on the two responses, should I have this:

# note that the background is using the standard deviation columns just as place
holder
RG<-read.maimages(targets$FileName,columns=list(Rf="C5_Signal_Median",Rb="C5_Signal_SD",Gf="C3_Signal_Median",Gb="C3_Signal_SD"),annotation=c('Sel_Crt','Probe_Seq','Fea
RG.no.background <- backgroundCorrect(RG,method='none')
MA.lnorm <- normalizeWithinArrays(RG.no.background,
method="loess",bg.method="none")

Thanks,
G

-- 

Systems Programmer
Yale Center for Medical Informatics
fax: 203-737-5708



Quoting M PEREZ <perezperezmm at yahoo.es>:

> 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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