Dear Listserv,
I have an unusual microarray data set -a RIP-ChIP data set- and would
like to use the "normexp" function (as found in limma) to background-
subtract my data (and I'll take it's log2 data transformation, too) -
but I don't want the automatic M and A value output that you can get
from limmaGUI. [This is solely because my data are not the least bit
normal and I cannot use limma to analyze them further.]
Is there a way for me to obtain the normexp (and transformed) data
from within R? Is is an "object" that I can "print" or "write" before
it gets converted to M values?
Thank you very much for your help,
Sincerely,
Alana
On Sun, Oct 4, 2009 at 9:20 PM, <adoty at="" umd.edu=""> wrote:
>
> Dear Listserv,
>
> I have an unusual microarray data set -a RIP-ChIP data set- and
would like to use the "normexp" function (as found in limma) to
background-subtract my data (and I'll take it's log2 data
transformation, too) - but I don't want the automatic M and A value
output that you can get from limmaGUI. ?[This is solely because my
data are not the least bit normal and I cannot use limma to analyze
them further.]
>
> Is there a way for me to obtain the normexp (and transformed) data
from within R? ?Is is an "object" that I can "print" or "write" before
it gets converted to M values?
>
Hi, Alana. Have a look at the help for the backgroundCorrect()
function in the limma package.
Sean
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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From: Sean Davis <seandavi@gmail.com>
Subject: Re: [BioC] getting normexp (and log2 transformed) values -
not
further-processed M values
Date: Mon, 5 Oct 2009 07:07:14 -0400
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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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> From: Sean Davis <seandavi at="" gmail.com="">
> Subject: Re: [BioC] getting normexp (and log2 transformed) values -
not
> further-processed M values
> Date: Mon, 5 Oct 2009 07:07:14 -0400
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>
> ------------------------------
Dear Dr. Smyth,
Thanks so much for your quick and helpful reply. Yes, I think you are
right to say "just use R!" I never had before I began to analyze my
RIP-CHiP data set (hence the non-standard use of limmaGUI) - but I
have indeed thoroughly read the limma user's manual (and I also tried
general R help documentation and the limma "user manual" to
investigate R more...)
Anyway, your help allowed me to solve a similar "output" problem in
another R package (eCADS). I also see that by using the
"exprs.MA(MA)" statement, I can recover normalized, log2 transformed
individual values for both the red and green channels for all my
arrays.
Thank you very much again for your help.
Sincerely,
Alana
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From: Gordon K Smyth <smyth@wehi.edu.au>
Subject: [BioC] getting normexp (and log2 transformed) values - not
further-processed M values
Date: Wed, 7 Oct 2009 09:25:42 +1100 (AUS Eastern Daylight Time)
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