[BioC] snapCGH: log2ratio

[caiwei at mdanderson.org]

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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|         |                       jhs1jjm at leeds.ac.uk|
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|         |                       10/08/2007 05:28 PM|
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  |      caiwei at mdanderson.org                                                                         |
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  |      "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>                             |
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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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