[BioC] limma how to ignoring background

[M PEREZ]

yeah, I think you are righ, you can choose between two options. if you use 
MA <- normalizeWithinArrays(RG, method="loess", bc.method="none") you can save just a little bit of code..

Manuel

Guoneng Zhong <guoneng.zhong at yale.edu> escribió:

Having looked at the help files for normalizeWithinArrays and backgroundCorrect,
I wonder if it is redundant to do both. I mean, if I do:

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

Do I need to do?:

MA <- normalizeWithinArrays(RG.no.background,method="loess",bc.method="none")

G

-- 

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



Quoting M PEREZ 
:

> sorry is bc.method="none" , instead bg.method... I misspelled it
>
> Manuel
>
> Guoneng Zhong escribió:
> 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
> :
>
> > 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 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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