[BioC] snapCGH: log2ratio

[jhs1jjm at leeds.ac.uk]

It adds the design component to your RGList/MAlist object. You would
either use:

> RG$design <- c(-1,-1) #Cy5 as ref channel

or

> RG$design <- c(1,1) #Cy3 as ref channel

This is required before you use the processCGH function

Regards
John

Quoting caiwei at mdanderson.org on Mon 08 Oct 2007 23:48:38 BST:

>
> John,
>
> Thanks,
>
> What does this command do (in the user guide)? does it affect
> Log2Ratio?
>
> RG$design<-c(-1,-1)
>
> Caimiao
>
>
>
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>   |Subject:
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>   |      Re: [BioC] snapCGH: log2ratio
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>----------------------------------------------------------------------------------------------------|
>
>
>
>
> Hi Caimiao,
>
> It is the log2(Cy5/Cy3) i.e log2(red/green). Depending on what you
> read
> into limma with read.maimages this will be the default estimates
> referred to in the vignette for your particular array or whatever you
> specified using the columns argument. Whether this is log(sample/ref)
> or log(ref/sample) depends on which way round you labeled the samples
> I
> guess. In aCGH expts the ref channel is normally dyed using Cy5 and
> test channel dyed using Cy3.
>
> Regards
>
> John
>
>
> Quoting caiwei at mdanderson.org on Mon 08 Oct 2007 19:24:20 BST:
>
> >
> > Dear list,
> >
> > Are the Log2 ratios in our MAlist the log ratios of test
> > sample/reference
> > sample? or the log ratios of Cy5/Cy3 as when we run
> > normalizeWithinArrays
> > in Limma?  I am confused when I read the section of  "Reading Data"
> > about
> > the design vector .
> >
> > Thanks,
> >
> > Caimiao
> >
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