[R] OT(slightly) - Tracking extended projects

Hi all, Most of the analyses I do are short little once-and-done type things that are easily encapsulated in a .Rnw file. However, I sometimes end up with projects that take an extended amount of time. Usually these projects are not easily encapsulated in an .Rnw file, so I have been using a

Re: [R] memory error with 64-bit R in linux

The dist object for the rows of the matrix will be 16000x16000, which if there are any copies will easily suck up all of your RAM. A more pertinent question is what use would a heatmap of that size be? How do you plan to visualize 16000 rows? In a pdf? You certainly couldn't publish such a

Re: [R] Me again, about the horrible documentation of tcltk

Hi Alberto, It took me approximately 20 seconds to find all the arguments for this function. Here were the steps I took. 1.) Look at R help page ?tkgetOpenFile 2.) Hmmm. Lots of functions, but little info. But wait, what's this? Details: [snip] There are far too many of these

Re: [R] [BioC] please recommend

Here is an excellent choice: http://www.amazon.com/exec/obidos/tg/detail/-/0387251464/qid=1129910139/sr=8-1/ref=pd_bbs_1/002-2566394-3995236?v=glances=booksn=507846 Best, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center

Re: [R] I never made any assumption athat anyone had any obligation to do anything

To add to Spencer's reply, I have two things. First, if you look back at your earlier list entries, Uwe asked you politely at least twice to read the posting guide. The reason for this is that the posting guide gives guidance to allow you to post questions that are clear enough to answer, and

Re: [R] Question on bioconductor: reading affymetrix data

This is a question that should be asked on the bioconductor mailing list rather than R-help. Quick answer: library(reposTools) install.packages2(whateverchiptypethisiscdf) Where you have to replace whateverchiptypethisiscdf with e.g., hgu133acdf. HTH, Jim James W. MacDonald Affymetrix and

Re: [R] Help w/ matrix calc

For row or column means with a matrix of any size, you will be much better served by using rowMeans() colMeans() Best, 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

Re: [R] Difference between normalizeWithinArrays and stat.ma

Since both of the packages you mention are part of Bioconductor, you would do well to re-post in the correct list ([EMAIL PROTECTED]). Best, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI

Re: [R] R help in Firefox on Windows XP

Works for me with Firefox 0.8. 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 Prof Brian Ripley [EMAIL PROTECTED] 06/17/04 02:10PM Works for me. Did it work with Firefox 0.8?

Re: [R] Tutorial for graphics

I don't know of a good tutorial, but I find that looking at ?par is usually good for answering most graphing questions. To resize axes, look at xlim and ylim under ?par. As for changing the axes, you can suppress the axes using e.g., for the x-axis xaxt=n in your plotting function call, and then

Re: [R] String problems

Plus, do you really want your system call to be system(c:\\dir g:\\simulation\\at) not sure what you want, but that is what you will get. 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

RE: [R] memory limit problem

If you check the max memory used, I bet it is the same as your memory.limit. Try memory.size(max=TRUE) to see how much memory was allocated. You also might try --max-mem-size=2000M. R will not actually be able to get all 2 Gb of ram, but I think it will be more than 1.5 Gb you are allowing now.

Re: [R] Where: package licenses

Note that package.descripton() is deprecated in R-1.9.0. You have to use packageDescription() instead. 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 Sundar Dorai-Raj

Re: [R] stop() vs. error() ?

And a closer examination of the help page would lead you to this: options(show.error.messages=FALSE) stop() which is what I believe you want Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI

Re: [R] memory problem

How many chips you can read is a function of how much RAM you have and what chip it is. On a unix/linux box you will be able to read in and process 143 of the HG-u95aV2 chips if you have about 2 Gb RAM. For the larger U133A chips (RAE/MOE are about the same size), you will probably need almost

RE: [R] Statistiques avec R

You can get a reasonable (if relatively comedic) translation of the page by doing a google search for 'Statistiques avec R', and then choosing Translate this page. Although oddly enough the translator only seems to do each page up to a point and then it reverts to French... Jim James W.

Re: [R] Newbie question: histogram

You don't make a histogram with a data.frame. You have to pass a vector of numeric values to hist(). If you want to make a histogram using a *column* of a df, you have to subset the df in the call to hist. hist(mydata[,1]) -or- hist(mydata[,year]) hist(mydata[,2]) - or- hist(mydata[,snow.cover])

Re: [R] Help in error : SAM function in library siggenes

siggenes is part of Bioconductor, and the author is Holger Schwender. You should ask Holger first ([EMAIL PROTECTED]), and the BioC list second. Best, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann

[R] problem with rcmd build R-devel

Hi All, I am having a problem with Rcmd build using R-devel on WinXP. If I try to build a package using the --binary flag, I get the following error: Error: cannot change to directory ' 'c:/TEMP/Rbuild.' ' Where is some number. I can get Rcmd build to work using R-1.7.1 and R-1.8.0,

Re: [R] Analyzing dendograms??

You are using the xlim and ylim arguments incorrectly. You should be doing something like xlim=c(0.5, nc+0.5), ylim=c(0.5, nc+0.5). The error message gave you this hint. HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical

Re: [R] Problem with parser and if/else

I'm trying to grasp this: if you're saying (or are you saying) that the only way to have if() know that an else will be present is to put it on the same line as the closing curly brace of the if() (compound) statement. But if I look at some code from, e.g., aov and lm, I see plenty

Re: [R] Round error?

You are doing something wrong.The p-value should be calculated using phyper alone. 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 Aurora Torrente [EMAIL PROTECTED]

Re: [R] index of max value ?

which(v==max(v)) should do the trick. 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 [EMAIL PROTECTED] 11/14/03 02:05PM Is there a function in R, which would return

Re: [R] Formatting axis label numbers on plots

Look at xaxt and yaxt under ?par, as well as ?axis. 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 M. Edward (Ed) Borasky [EMAIL PROTECTED] 11/12/03 17:56 PM Is there

Re: [R] FDR in p.adjust

There is no threshold for fdr. The adjusted p-values give the expected proportion of false positives for all comparisons with similar p-values or smaller. In other words, if you choose a p-value of 0.05, you would expect that ~5% of the tests with a p-value of 0.05 or smaller are false positives.

Re: [R] how to set missing values in R

x[x0] - NA 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 Yulei He [EMAIL PROTECTED] 10/27/03 04:05PM Hi, there. Can I ask how to set up missing values in R? Suppose I want to

Re: [R] repeating colors in graph 2

Thomas Lumley [EMAIL PROTECTED] 10/23/03 04:26PM On Thu, 23 Oct 2003, James MacDonald wrote: I believe you want plot(blah blah, col=palette(rainbow(13))) No. palette() sets the default palette, so eg palette(rainbow(13)) plot(1:13,col=1:13) will plot in the new palette. -thomas

Re: [R] problems with Affy

You need to use the devel versions of Bioconductor packages with R-1.8.0 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 r.ghezzo [EMAIL PROTECTED] 10/24/03 09:55AM I just

Re: [R] repeating colors in graph 2

I believe you want plot(blah blah, col=palette(rainbow(13))) 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 Anna Pryor [EMAIL PROTECTED] 10/23/03 02:19PM I've tried

Re: [R] changing the the column header in a data.frame

If you data.frame is called df, then names(df) - c(new names here) You can also do individual names names(df)[1] - new name for first column HTH Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor

Re: [R] Source package installation for WinXPpro

You need to make sure that all the tools are in your path, with the R tools before perl and mingw. Set this by right clicking My Computer, then properties, advanced, environment variables, then edit the path in the system variables window. Once you have done that, you should be able to download

Re: [R] I need your help....

This is a question for the Bioconductor listserv, not R-help. In addition, all current versions of affy will automagically download and install any cdfenvs that you may need, so there is no need to do this manually. If anything, you may need to update your version of affy. Jim James W.

[R] R-1.8.0 memory.limit()

Using R-1.8.0 (d/l and compiled on 2003-10-01) on WinXP, I seem to be unable to determine the maximum memory allocated to R. The help still says to use memory.limit(size=NA), but this returns the value NA. In addition, I have set --max-mem-size=2G but I run out of memory somewhere around 500Mb

Re: [R] Still Cannot Install rimage in R-1.7.1 (RH 9.0) Even With fftwInstalled

Aren't the headers usually in the devel package (e.g., fftw-devel-2.1.5-0.dag.rh73.i386.rpm)? You might try installing the devel package too. 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

Re: [R] sas.get problem

It's actually in the Hmisc package. The error looks like Hmisc hasn't been attached yet, so you might try library(Hmisc) first. In addition, it does appear from the help file that you need SAS installed to output the ASCII files that are required to import the data. HTH, Jim James W.

Re: [R] generic function object

getMethods(normalize) should do the trick. Best, 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 Mathieu Drapeau [EMAIL PROTECTED] 09/30/03 02:14PM Hi, I would like to

Re: [R] Downloading LME4?

I don't think there is a compiled version of this library, so you will have to compile and install yourself. See question 3.1 of the R for Windows FAQ. In addition, the fact that there is not a compiled version on CRAN may indicate a problem with this package on Windows. HTH, Jim James W.

Re: [R] R-help: beginner question

If you read the data into a data frame, you should be able to simply pass the name of the data frame in a call to boxplot. my.data - read.delim(mytext.txt) boxplot(my.data) If you only want a boxplot of column 5 boxplot(my.data[,5]) See ?boxplot for other options to make the boxplot look the

Re: [R] Variance Computing- - HELP!!!!!!!!!!!!!!!!!!

I think you are confused. As sample size increases, the variance of an estimate based on that sample will decrease asymtotically to zero (e.g., the standard error of the mean will go to zero). However the variance of the sample itself will not change. Any difference you see in your data is simply

Re: [R] How to copy and paste a R plot onto Word (or PowerPoint)

Either ?savePlot and import using Import -- Picture -- File in Word/PowerPoint or right click, copy as..., and paste in Word/Power point 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

Re: [R] ^ operation much slower in R 1.7.1 than in R 1.7.0 ???

I get similar results as Philippe on WinXP (1.33 GHz laptop, 512 Mb RAM). R 1.7.1 2.86 sec 7.82 sec R 1.7.0 0.64 sec 1.64 sec 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

RE: [R] R won't connect to the internet on SUSE Linux 8.1

HTTP_PROXY issues aside, if all you want to do is install Bioconductor, simply download the latest bioconductor_xx.tar.gz and use R CMD INSTALL. Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI

Re: [R] Matrix manipulation - dropping rows based on a query

tst - apply(my.mat, 2, mean) 1 my.mat[,tst] Will return only columns with mean 1 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 [EMAIL PROTECTED] 07/22/03 01:53PM I

Re: [R] Line plot help

Segments should do what you want. Try ?segments for help. 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 Carlos Rios [EMAIL PROTECTED] 07/16/03 12:26PM I was wondering if

Re: [R] How to read in data

You probably need to change the directory to the one that contains the text file you are reading in. This is done under the File menu. 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