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Question: getting normexp (and log2 transformed) values - not further-processed M values
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gravatar for adoty@umd.edu
8.7 years ago by
adoty@umd.edu30 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? Thank you very much for your help, Sincerely, Alana
ADD COMMENTlink modified 8.7 years ago • written 8.7 years ago by adoty@umd.edu30
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gravatar for Sean Davis
8.7 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
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
ADD COMMENTlink written 8.7 years ago by Sean Davis21k
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gravatar for adoty@umd.edu
8.7 years ago by
adoty@umd.edu30 wrote:
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 -------------- next part -------------- An embedded message was scrubbed... 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 Size: 3187 URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20091005="" 26329477="" attachment.eml="">
ADD COMMENTlink written 8.7 years ago by adoty@umd.edu30
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gravatar for Gordon Smyth
8.7 years ago by
Gordon Smyth33k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth33k wrote:
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 > > -------------- next part -------------- > An embedded message was scrubbed... > 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 > Size: 3187 > URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 200910="" 05="" 26329477="" attachment-0001.eml=""> > > ------------------------------
ADD COMMENTlink written 8.7 years ago by Gordon Smyth33k
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gravatar for adoty@umd.edu
8.7 years ago by
adoty@umd.edu30 wrote:
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 -------------- next part -------------- An embedded message was scrubbed... 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) Size: 5003 URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20091007="" ae4b6a5c="" attachment.eml="">
ADD COMMENTlink written 8.7 years ago by adoty@umd.edu30
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