[BioC] Limma - write table??

[J.delasHeras at ed.ac.uk]

Quoting alison waller <alison.waller at utoronto.ca>:

> Hi All,
>
>
>
> I have read in my .gpr files, done normalization between and within arrays.
> I would now like to export my normalized R and G values to a file that I can
> save.
>
>
>
> I can export the R and the G values separately, but I would like a table as
> below:
>
> SpotName(fromGALfile)            R          G
>
>
>
> I used >write.table(RG$R,file="myout.txt",sep="\t").
>
>
>
> So basically, can I specify that I want to include the gene information from
> the gal file instead of just listing the values my number, and can I print
> out R and G?
>
>
>
> Thanks,
>
>
>
> Alison


Hi Alison,

Sean showed you how to export a table with the values you want. I'm  
just a little confused by what you mean about the "normalised R and G  
values".

Usually we deal with M values, after normalisation, where  
M=log2(Cy5/Cy3). These will be stored in a MAList object (what you get  
after normalisation).

If you want to see the normalised R and G values, you can obtain those  
from the MAList. The function 'RG.MA' does that. You might know that  
already, but just in case!

Jose

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Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
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