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

[adoty at umd.edu]

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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