[BioC] getting normexp (and log2 transformed) values - not further-processed M values

[Gordon K Smyth]

Dear Alana,

Since you want to do your own customized analysis of the data, which is 
different from what limmaGUI provides, you will find it easier to use the 
command-line limma package rather than limmaGUI.  All objects created will 
be quite transparent.

If you want to output values from an RGList object to a text file, you can 
type

  write.table(file="yourfilenamered.txt",RG$R)

and

  write.table(file="yourfilenamegreen.txt",RG$G)

However I find it hard to believe this is a good idea.  Better to find out 
how to do what you want in R.  I suspect you're making things harder for 
yourself than it needs to be.

Best wishes
Gordon

> Date: Mon,  5 Oct 2009 19:36:38 -0400 (EDT)
> From: <adoty at umd.edu>
> Subject: [BioC] getting normexp (and log2 transformed) values - not
> 	further-processed M values
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <20091005193638.ATB49372 at po5.mail.umd.edu>
> Content-Type: text/plain; charset="us-ascii"
>
>
> Dear Scott et al.
>
> Thank you very much for the information. After reading both the 
> limma.pdf and the usersguide.pdf (and playing around with my Windows R 
> console), I now know that by typing "fix(RG)" in limmaGUI's "Evaluate R 
> Code" tab, I can get the RG object to display itself in some form...
>
>
> I do, though, have 3 remaining (and hopefully final) questions on this topic:
>
> 1) what's the difference between RG and RGList?  I see them both used in 
> the help/example files and I can't tell which one has the output I'd 
> like from "backgroundCorrect" (-again, I'd like to obtain the normexp 
> backgrounded-corrected values, using an offset, for both the R and G 
> channels from each of my 5 arrays)
>
> 2) will the values in whichever of these "objects" I need [RG or RGList] 
> be log2 transformed already?  I'm not sure if this is automaticaly done 
> or not...
>
> 3) when I look at the corrected data with "fix(RG)", it's in matrix 
> form, right?  How can I get the data into, say, a form readable by 
> Excel?  I think I can get some useful output with "show(RG)," too - but 
> in this form it would require a lot of copying/pasting to get into Excel 
> (and by default, not all the lines are shown).
>
>
> Thank you VERY much for any help someone may be able to provide.  I am 
> trying to learn what I can on my own! - but it's going a bit more slowly 
> than I'd like some answers by...
>
>
> Sincerely,
> Alana Doty
> University of Maryland
>
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