[BioC] Extracting Single Channel Intensities in limma

[Sean Davis]

Mick,

Is there no way to do this with an appropriate contrast matrix?  That 
seems a safer/more appropriate way of using your two-channel data.

Sean

On Oct 1, 2004, at 7:35 AM, michael watson (IAH-C) wrote:

> Hi
>
> I have performed print-tip loess normalisation followed by quantile
> normalisation in limma.  I have then converted the resulting MAList
> object back to an RGList object using RG.MA().  I now want to extract
> the single channel intensities from this normalised RGList object to
> create *new* RGList objects which represent comparisons between samples
> that were not made on the arrays directly.
>
> However, as RG.MA gives me log2(intensity) back rather than raw
> intensity, I presume I need to un-log this data before sending it down
> my normal analysis pipeline of RGList -> MAList -> lmFit(MAList) ->
> eBayes() -> topTable() ??
>
> Thanks
> Mick
>
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