Limma Documentation: normalization functions
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Paul Boutros ▴ 200
@paul-boutros-98
Last seen 10.2 years ago
Hi all, I'm trying to get familiar with the limma package, but I've run into something I don't understand. After I load the package, if I type: ?normalizeWithinArrays The documentation doesn't give a list of available normalization methods. Instead it refers me to: "An overview of LIMMA functions for normalization is given in 4.Normalization." However, when I go to the "limma: Linear Models for Microarray Data User's Guide" (a pdf in the limma folder of my /library) there is no section on normalization there. I also didn't see a vignette for limma. Since nobody else has asked about this, I figure the documentation is here somewhere, and I just don't know where to find it! Any guidance much appreciated. Paul limma user's Guide is 19-May-2003. limma is 1.0.8 R is 1.7.1 OS is WinXP SP1 ---------------------------------------- This mail sent through www.mywaterloo.ca
Microarray Normalization GO limma Microarray Normalization GO limma • 1.9k views
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@gordon-smyth
Last seen 3 hours ago
WEHI, Melbourne, Australia
Dear Paul, At 05:24 AM 9/08/2003, Paul Boutros wrote: >Hi all, > >I'm trying to get familiar with the limma package, but I've run into >something >I don't understand. After I load the package, if I type: >?normalizeWithinArrays >The documentation doesn't give a list of available normalization methods. >Instead it refers me to: >"An overview of LIMMA functions for normalization is given in >4.Normalization." I have reproduced below the first few paragraphs of the help document that one gets by typing ?normalizeWithinArrays. As you can see, documentation for the argument "method" gives a list of available normalization methods. There are further details further down in the document under "Details". The line that you have quoted is the second last line of the help document. It would seem that you are only reading the last two lines of the document. ------------------ normalizeWithinArrays package:limma R Documentation Normalize Within Arrays Description: Normalize the expression log-ratios for one or more two-colour spotted microarray experiments so that the log-ratios average to zero within each array or sub-array. Usage: normalizeWithinArrays(object, layout, method="printtiploess", weights=object$weights, span=0.3, iterations=4, controlspots=NULL, df=5, robust="M") MA.RG(object) Arguments: object: object of class `list', `RGList' or `MAList' containing two-color microarray data layout: list specifying the dimensions of the spot matrix and the grid matrix method: character string specifying the normalization method. Choices are `"none"', `"median"', `"loess"', `"printtiploess"', `"composite"' and `"robustspline"'. A partial string sufficient to uniquely identify the choice is permitted. If no method is recognized, then unnormalized M and A-values are returned. ------------------ rest of document deleted ------------------- >However, when I go to the "limma: Linear Models for Microarray Data User's >Guide" (a pdf in the limma folder of my /library) there is no section on >normalization there. I also didn't see a vignette for limma. The User's Guide is the vignette for LIMMA. Although there isn't a separate section on normalization, there are four complete data case studies all of which include commands for normalization. > Since nobody >else has asked about this, I figure the documentation is here somewhere, >and I >just don't know where to find it! Any guidance much appreciated. > >Paul > >limma user's Guide is 19-May-2003. >limma is 1.0.8 It might be a good idea to install the development version of limma which is up to version 1.1.10. The html version of the User's Guide is also updated somewhat in the development version. Regards Gordon >R is 1.7.1 >OS is WinXP SP1
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Hi Sir, > -----Original Message----- > From: Gordon Smyth [mailto:smyth@wehi.edu.au] > Sent: Saturday, August 09, 2003 4:09 AM > To: Paul.Boutros@utoronto.ca > Cc: bioconductor@stat.math.ethz.ch > Subject: Re: [BioC] Limma Documentation: normalization functions > > > Dear Paul, > > At 05:24 AM 9/08/2003, Paul Boutros wrote: > >Hi all, > > > >I'm trying to get familiar with the limma package, but I've run into > >something > >I don't understand. After I load the package, if I type: > >?normalizeWithinArrays > >The documentation doesn't give a list of available normalization methods. > >Instead it refers me to: > >"An overview of LIMMA functions for normalization is given in > >4.Normalization." > > I have reproduced below the first few paragraphs of the help > document that > one gets by typing ?normalizeWithinArrays. As you can see, documentation > for the argument "method" gives a list of available normalization > methods. > There are further details further down in the document under > "Details". The > line that you have quoted is the second last line of the help > document. It > would seem that you are only reading the last two lines of the document. > > ------------------ > normalizeWithinArrays package:limma R Documentation > > Normalize Within Arrays > > Description: > > Normalize the expression log-ratios for one or more two-colour > spotted microarray experiments so that the log-ratios average to > zero within each array or sub-array. > > Usage: > > normalizeWithinArrays(object, layout, method="printtiploess", > weights=object$weights, span=0.3, iterations=4, controlspots=NULL, df=5, > robust="M") > MA.RG(object) > > Arguments: > > object: object of class `list', `RGList' or `MAList' containing > two-color microarray data > > layout: list specifying the dimensions of the spot matrix and the > grid matrix > > method: character string specifying the normalization method. Choices > are `"none"', `"median"', `"loess"', `"printtiploess"', > `"composite"' and `"robustspline"'. A partial string > sufficient to uniquely identify the choice is permitted. If > no method is recognized, then unnormalized M and A-values are > returned. > ------------------ rest of document deleted ------------------- This is weird: I get totally different output. I've appended mine below. Is this just a version issue, or is it something I should worry about? ------------------ Begin document ------------------------------ normalizeWithinArrays package:limma R Documentation Normalize Within Arrays - generic Description: A generic function which normalizes microarray data. Normalization is intended to remove from the expression measures any systematic trends which arise from the microarray technology rather than from differences between the probes or between the target RNA samples hybridized to the arrays. Usage: normalizeWithinArrays(object,...) Arguments: object: a data object containing microarray data ...: any other arguments Methods: Methods are defined in limma for `object' an object of class `list', `RGList' or `MAList'. Type `showMethods("normalizeBetweenArrays")' at the R prompt for a complete list of classes for which methods are defined. Author(s): Gordon Smyth See Also: An overview of LIMMA functions for normalization is given in 4.Normalization. See also `normalizeBetweenArrays' and `maNorm' in the marrayNorm package. ------------------ End document -------------------------------- > >However, when I go to the "limma: Linear Models for Microarray > Data User's > >Guide" (a pdf in the limma folder of my /library) there is no section on > >normalization there. I also didn't see a vignette for limma. > > The User's Guide is the vignette for LIMMA. Although there isn't > a separate > section on normalization, there are four complete data case > studies all of > which include commands for normalization. > > > Since nobody > >else has asked about this, I figure the documentation is here somewhere, > >and I > >just don't know where to find it! Any guidance much appreciated. > > > >Paul > > > >limma user's Guide is 19-May-2003. > >limma is 1.0.8 > > It might be a good idea to install the development version of limma which > is up to version 1.1.10. The html version of the User's Guide is also > updated somewhat in the development version. Okay, will do. Thanks! Paul > Regards > Gordon > > >R is 1.7.1 > >OS is WinXP SP1
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@gordon-smyth
Last seen 3 hours ago
WEHI, Melbourne, Australia
Dear Paul, At 04:38 AM 10/08/2003, Paul Boutros wrote: > > -----Original Message----- > > From: Gordon Smyth [mailto:smyth@wehi.edu.au] > > Sent: Saturday, August 09, 2003 4:09 AM > > To: Paul.Boutros@utoronto.ca > > Cc: bioconductor@stat.math.ethz.ch > > Subject: Re: [BioC] Limma Documentation: normalization functions > > > > > > Dear Paul, > > > > At 05:24 AM 9/08/2003, Paul Boutros wrote: > > >Hi all, > > > > > >I'm trying to get familiar with the limma package, but I've run into > > >something > > >I don't understand. After I load the package, if I type: > > >?normalizeWithinArrays > > >The documentation doesn't give a list of available normalization methods. > > >Instead it refers me to: > > >"An overview of LIMMA functions for normalization is given in > > >4.Normalization." > > > > I have reproduced below the first few paragraphs of the help > > document that > > one gets by typing ?normalizeWithinArrays. As you can see, documentation > > for the argument "method" gives a list of available normalization > > methods. > > There are further details further down in the document under > > "Details". The > > line that you have quoted is the second last line of the help > > document. It > > would seem that you are only reading the last two lines of the document. ... help document deleted >This is weird: I get totally different output. I've appended mine below. >Is this just a version issue, or is it something I should worry about? Ah, I can see what is happening now. My apologies. In the BioC Release 1.2 version of limma, which was limma 1.0.8, I wrote normalizeWithinArrays as a new-style generic function. That means that normalizeWithinArrays doesn't do anything itself, it just passes the information on to more specific functions called "Methods" which actually do the work, depending on the type of data which you input. What you were supposed to do was to see that normalizeWithinArrays accepts RGList objects and then type ?normalizeWithinArrays.RGList for the more detailed information. (Alternatively you could type helpMethods("normalizeWithinArrays") which would give you a menu of more detailed help pages, or else use the html contents help page for limma.) You are far from the only one who found this too obscure. I decided that there is no good way to write documentation for new-style generic functions within the R help system as it currently stands, so I have gone back to a programming style in the development version of limma which does not use the formal object-orientated programming system. This means that the documentation for functions like normalizeWithinArrays is now much more direct and you should find it more transparent. I recommend that you get limma 1.1.10. An added advantage is that the normalization routines are now much faster and more robust. If you can't get it from the Bioconductor.org www site, then you can get it from http://bioinf.wehi.edu.au/limma/. If you have installation rights on your computer you may be able to type install.packages("limma",contriburl="http://bioinf.wehi.edu.au/limma") in R to get automatic installation of the latest version. Best wishes Gordon >------------------ Begin document ------------------------------ >normalizeWithinArrays package:limma R Documentation > >Normalize Within Arrays - generic > >Description: > > A generic function which normalizes microarray data. Normalization > is intended to remove from the expression measures any systematic > trends which arise from the microarray technology rather than from > differences between the probes or between the target RNA samples > hybridized to the arrays. > >Usage: > > normalizeWithinArrays(object,...) > >Arguments: > > object: a data object containing microarray data > > ...: any other arguments > >Methods: > > Methods are defined in limma for `object' an object of class > `list', `RGList' or `MAList'. > > Type `showMethods("normalizeBetweenArrays")' at the R prompt for a > complete list of classes for which methods are defined. > >Author(s): > > Gordon Smyth > >See Also: > > An overview of LIMMA functions for normalization is given in > 4.Normalization. > > See also `normalizeBetweenArrays' and `maNorm' in the marrayNorm > package. >------------------ End document -------------------------------- ... earlier correspondence deleted
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