On Sat, May 8, 2010 at 6:22 AM, Lloyd, Bryony
<Bryony.Lloyd@liverpool.ac.uk>wrote:

>
> Hi,
>
> Many thanks for your kind help. My first day with Bioconductor has been
> interesting to say the least. I have created my RGList from my normalised
> MAList, and have managed to write the $R and $G data to file by creating
> sublists, representing the data as a matrix (as.matix) and writing this to
> file. As this does not work with text I need to get hold of the $genes data
> somehow I would be delighted if someone could help.
>
>
If your RGlist is called RG:

write.table(RG$genes,"genes.txt",sep="\t",col.names=TRUE,row.names=FALSE)

Sean


> ________________________________________
> From: Sean Davis [seandavi@gmail.com]
> Sent: 07 May 2010 17:44
> To: Lloyd, Bryony
> Cc: bioconductor@stat.math.ethz.ch
> Subject: Re: [BioC] Obtaining Normalised Signal intensities
>
> On Fri, May 7, 2010 at 12:04 PM, Lloyd, Bryony
> <Bryony.Lloyd@liverpool.ac.uk> wrote:
> > Hi,
> >
> > I was hoping that someone might be able to help me. I have inherited data
> from 4 Agilent arrays. I would like to recover and output to file the
> normalised signal intensity of the Cy3 and Cy5 data if possible, rather than
>  the log ratio of each. If anyone can suggest a way to do this I would be
> most grateful.
> > As the MA can be use by plotDensities() to show the effect of
> normalisation upon signal intensities, I'm hoping that this will be
> possible.
> > Hope you can help.
>
> See the RG.MA in limma, assuming that you have an MAList.  If not,
> you'll need to be more specific about what you have.
>
> Sean
>

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