Question: limma
0
gravatar for Peter Wilkinson
15.0 years ago by
Peter Wilkinson80 wrote:
Hi there, I would like to explore the idea of creating a function that is a modification of the normalizeWithinArrays() with printtiploess option of the limma package. We are spot quality control prior to normalization which results in some genes being dropped. Once that happens then we no longer have complete sub-grids; normlizeWithinArrays will nor longer work with the printtip loess option. So I wish to make a modification to the normalizeWithinArrays function that will re-index each sub-grid, so that the print top loess can be performed. So I have been looking for the source code for limma, but it seams to be unavailable since the package is distributed as a binary. I have checked the author's page but its not there either. I would like permission to look into the limma package source code and re-factor the normalizeWithinArrays() function to do what I want. Can somebody send me the source code ? Peter
normalization limma • 486 views
ADD COMMENTlink modified 15.0 years ago by daniela.marconi@libero.it100 • written 15.0 years ago by Peter Wilkinson80
Answer: limma
0
gravatar for James W. MacDonald
15.0 years ago by
United States
James W. MacDonald50k wrote:
The code is available to you right now. The easiest way to get it is to type normalizeWithinArrays at an R prompt, copy and paste into your favorite editor. If you want the source code with any comments that may exist, you will have to download the source version of limma, untar and gunzip it and then open norm.R in your favorite editor. HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Peter Wilkinson <pwilkinson@videotron.ca> 07/14/04 05:36PM >>> Hi there, I would like to explore the idea of creating a function that is a modification of the normalizeWithinArrays() with printtiploess option of the limma package. We are spot quality control prior to normalization which results in some genes being dropped. Once that happens then we no longer have complete sub-grids; normlizeWithinArrays will nor longer work with the printtip loess option. So I wish to make a modification to the normalizeWithinArrays function that will re-index each sub-grid, so that the print top loess can be performed. So I have been looking for the source code for limma, but it seams to be unavailable since the package is distributed as a binary. I have checked the author's page but its not there either. I would like permission to look into the limma package source code and re-factor the normalizeWithinArrays() function to do what I want. Can somebody send me the source code ? Peter _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
ADD COMMENTlink written 15.0 years ago by James W. MacDonald50k
Answer: limma
0
gravatar for Peter Wilkinson
15.0 years ago by
Peter Wilkinson80 wrote:
Ah yes you are right I can type the function in. I would prefer to get the source code for the comments. The problem is that I did not notice where the source code resides. I have downloaded from the source link from the bioconductor site, and I will try that. Thanks for your input. Peter At 10:44 AM 7/15/2004, James MacDonald wrote: >The code is available to you right now. The easiest way to get it is to >type normalizeWithinArrays at an R prompt, copy and paste into your >favorite editor. If you want the source code with any comments that may >exist, you will have to download the source version of limma, untar and >gunzip it and then open norm.R in your favorite editor. > >HTH, > >Jim > > > >James W. MacDonald >Affymetrix and cDNA Microarray Core >University of Michigan Cancer Center >1500 E. Medical Center Drive >7410 CCGC >Ann Arbor MI 48109 >734-647-5623 > > >>> Peter Wilkinson <pwilkinson@videotron.ca> 07/14/04 05:36PM >>> >Hi there, > >I would like to explore the idea of creating a function that is >a modification of the normalizeWithinArrays() with printtiploess >option of >the limma package. > >We are spot quality control prior to normalization which results in >some >genes being dropped. Once that happens then we no longer have complete > >sub-grids; normlizeWithinArrays will nor longer work with the printtip > >loess option. So I wish to make a modification to the >normalizeWithinArrays >function that will re-index each sub-grid, so that the print top loess >can >be performed. > >So I have been looking for the source code for limma, but it seams to >be >unavailable since the package is distributed as a binary. I have >checked >the author's page but its not there either. > >I would like permission to look into the limma package source code and > >re-factor the normalizeWithinArrays() function to do what I want. > >Can somebody send me the source code ? > >Peter > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
ADD COMMENTlink written 15.0 years ago by Peter Wilkinson80
On Thu, Jul 15, 2004 at 03:51:53PM -0400, Peter Wilkinson wrote: > > Ah yes you are right I can type the function in. I would prefer to get the > source code for the comments. The problem is that I did not notice where > the source code resides. I have downloaded from the source link from the > bioconductor site, and I will try that. > > Thanks for your input. R packages are basically distributed in two formats: source and binary. Unix versions are always source and windows are always binary. As long as you are only interested in the R code, you can - as James said - always get the source from within R (although it might be difficult depending on what function you want access to. "getAnywhere()" is nice to know about"). I think (99% sure) that you cannot get the C code from within R. The thing to do is retriving the source tarballs. Eg. getting the source code for biobase may be done by pointing your webbrowser at "www.bioconductor.org" , click "devel packages", "biobase" and finally "source package download". Standard R packages may be gotten from CRAN in a similar fashion. But if you are simply looking for the R code, the thing to do is probably accesing it through R. /Kasper > At 10:44 AM 7/15/2004, James MacDonald wrote: > >The code is available to you right now. The easiest way to get it is to > >type normalizeWithinArrays at an R prompt, copy and paste into your > >favorite editor. If you want the source code with any comments that may > >exist, you will have to download the source version of limma, untar and > >gunzip it and then open norm.R in your favorite editor. > > > >HTH, > > > >Jim > > > > > > > >James W. MacDonald > >Affymetrix and cDNA Microarray Core > >University of Michigan Cancer Center > >1500 E. Medical Center Drive > >7410 CCGC > >Ann Arbor MI 48109 > >734-647-5623 > > > >>>> Peter Wilkinson <pwilkinson@videotron.ca> 07/14/04 05:36PM >>> > >Hi there, > > > >I would like to explore the idea of creating a function that is > >a modification of the normalizeWithinArrays() with printtiploess > >option of > >the limma package. > > > >We are spot quality control prior to normalization which results in > >some > >genes being dropped. Once that happens then we no longer have complete > > > >sub-grids; normlizeWithinArrays will nor longer work with the printtip > > > >loess option. So I wish to make a modification to the > >normalizeWithinArrays > >function that will re-index each sub-grid, so that the print top loess > >can > >be performed. > > > >So I have been looking for the source code for limma, but it seams to > >be > >unavailable since the package is distributed as a binary. I have > >checked > >the author's page but its not there either. > > > >I would like permission to look into the limma package source code and > > > >re-factor the normalizeWithinArrays() function to do what I want. > > > >Can somebody send me the source code ? > > > >Peter > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor@stat.math.ethz.ch > >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- Kasper Daniel Hansen, Research Assistant Department of Biostatistics, University of Copenhagen
ADD REPLYlink written 15.0 years ago by Kasper Daniel Hansen630
Answer: limma
0
gravatar for James Wettenhall
15.0 years ago by
James Wettenhall1000 wrote:
Hi Peter, The source code of limma is certainly available, at: http://bioinf.wehi.edu.au/limma/limma_1.7.2.tar.gz You can unzip and untar the package with: tar zxvf limma_1.7.2.tar.gz or gunzip limma_1.7.2.tar.gz tar xvf limma_1.7.2.tar If you are using Windows, you can obtain tar and gunzip from the Rtools bundle at: http://www.murdoch-sutherland.com/Rtools/ (Or you may be able to unzip a tarball with Winzip, but I'd recommend using tar and gunzip.) If you are using Mac, tar and gunzip should be available in the apple developer tools. Hopefully you realize that normalizeWithinArrays can already accept weights, so you can give some spots zero weight if you want, then exclude them completely after normalization. One comment about typing the name of an R function and pressing enter is that sometimes (especially on Windows) if the source code of the function contains an escpaed character like a tab: sep="\t" it may be displayed as: sep=" " when you type the function name and press enter within R. For an example of this, try typing the name of the limma function read.maimages and pressing Enter, then scroll back up and look at the 'sep' argument. Regards, James
ADD COMMENTlink written 15.0 years ago by James Wettenhall1000
Answer: limma
0
gravatar for Gordon Smyth
15.0 years ago by
Gordon Smyth38k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth38k wrote:
Others have pointed out to you how to access the source code, but there is no real need to make the modification to limma that you seeking to do. Instead of removing problem genes from the data set, simply assign them weight zero. This is exactly equivalent to removing them in the normalization step but avoids having to re-index the sub-grids. Gordon > Hi there, > > I would like to explore the idea of creating a function that is > a modification of the normalizeWithinArrays() with printtiploess option > of > the limma package. > > We are spot quality control prior to normalization which results in some > genes being dropped. Once that happens then we no longer have complete > sub-grids; normlizeWithinArrays will nor longer work with the printtip > loess option. So I wish to make a modification to the > normalizeWithinArrays > function that will re-index each sub-grid, so that the print top loess can > be performed. > > So I have been looking for the source code for limma, but it seams to be > unavailable since the package is distributed as a binary. I have checked > the author's page but its not there either. > > I would like permission to look into the limma package source code and > re-factor the normalizeWithinArrays() function to do what I want. > > Can somebody send me the source code ? > > Peter
ADD COMMENTlink written 15.0 years ago by Gordon Smyth38k
Hi there, Thank you for your input. In fact this morning I tried just that, setting the gene to 0, and I found that to work. Peter At 09:57 PM 7/15/2004, Gordon K Smyth wrote: >Others have pointed out to you how to access the source code, but there is >no real need to make the modification to limma that you seeking to do. >Instead of removing problem genes from the data set, simply assign them >weight zero. This is exactly equivalent to removing them in the >normalization step but avoids having to re-index the sub-grids. > >Gordon > > > Hi there, > > > > I would like to explore the idea of creating a function that is > > a modification of the normalizeWithinArrays() with printtiploess option > > of > > the limma package. > > > > We are spot quality control prior to normalization which results in some > > genes being dropped. Once that happens then we no longer have complete > > sub-grids; normlizeWithinArrays will nor longer work with the printtip > > loess option. So I wish to make a modification to the > > normalizeWithinArrays > > function that will re-index each sub-grid, so that the print top loess can > > be performed. > > > > So I have been looking for the source code for limma, but it seams to be > > unavailable since the package is distributed as a binary. I have checked > > the author's page but its not there either. > > > > I would like permission to look into the limma package source code and > > re-factor the normalizeWithinArrays() function to do what I want. > > > > Can somebody send me the source code ? > > > > Peter
ADD REPLYlink written 15.0 years ago by Peter Wilkinson80
Answer: limma
0
gravatar for daniela.marconi@libero.it
15.0 years ago by
Hi I'm using limma for an affymetrix dataset. For summarize which is the most relavant differential expressed genes I use classifyTestsF() and I extract up-regulated and down-regulated genes. At the same time i look at the results of the fit with topTable() (sorted by B). But the genes are not the same. Is it possible? Why? What is the better solution, to summarize my results, between B and F-statistics? Thanks Daniela Marconi
ADD COMMENTlink written 15.0 years ago by daniela.marconi@libero.it100
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