Re: [R] data formatting: from rows to columns

)[1]) cat(paste(mat[i,], collapse=\n), \n\n, file=con) close(con) Best, Jim Cheers, Fede -- James W. MacDonald, M.S. Biostatistician 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] Synchronzing workspaces

up with projects spread around the various machines I work on. I find that placing the directories on a server and reading them remotely tends to slow things down. thanks, Eric -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer

Re: [R] problems saving and loading (PLMset) objects

, reproducible code. -- James W. MacDonald, M.S. Biostatistician 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-help@stat.math.ethz.ch mailing list

Re: [R] problems saving and loading (PLMset) objects

] character Best, Jim Quin Wills wrote: Erm, Jim I am loading in the affyPLM package first (when needed) and this was a question based on loading/saving R objects. PLMset was an example. Many thanks, Quin -Original Message- From: James W. MacDonald [mailto:[EMAIL PROTECTED] Sent

Re: [R] Q: obtaining non-transparent background in png

://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500

Re: [R] R and Genotyping

, reproducible code. -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ** Electronic Mail is not secure

Re: [R] sma package, and MouseArray data set

other attached packages: sma 0.5.15 -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive Ann Arbor MI 48109 734-647-5623 ** Electronic Mail is not secure, may

Re: [R] Read in 250K snp chips

or workaround for these large snp chips? Oligo is a Bioconductor package, so you should probably direct questions on the Bioconductor-help listserve rather than R-help. Best, Jim -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center

Re: [R] Greek symbols in xtable rows

and provide commented, minimal, self-contained, reproducible code. -- James W. MacDonald, M.S. Biostatistician 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] question on suppressing error messages with Rmath library

-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive

Re: [R] RODBC Excel sqlQuery insert into

. There are some good examples of how to do things that come with the package. Searching the R-help archives should also come up with some good examples. Best, Jim -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center

Re: [R] color key of heatmap.2

! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- James W. MacDonald, M.S

Re: [R] How to open more windows to make more graphs at once!

-guide.html and provide commented, minimal, self-contained, reproducible code. -- James W. MacDonald, M.S. Biostatistician 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] topTable function from LIMMA

@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core

Re: [R] Removing directory?

-guide.html and provide commented, minimal, self-contained, reproducible code. -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive Ann Arbor MI 48109 734-647-5623 ** Electronic Mail

Re: [R] Efficient way to repeat rows (or columns) of a matrix?

/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive Ann Arbor MI 48109

Re: [R] PlotAffyRNAdeg on Estrogen Data

://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500

Re: [R] Problems with 'delay'/'delayedAssign' when installing data package

@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray

Re: [R] graphics and 'layout' question

the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor

Re: [R] Successive Graphs

/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center

Re: [R] Question on AffyBatch

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan

Re: [R] Local library under Windoze.

@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray

Re: [R] R Training in the USA

! http://www.R-project.org/posting-guide.html -- James W. MacDonald, M.S. Biostatistician 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] limma - OneWayAnova

/posting-guide.html -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ** Electronic Mail is not secure, may

Re: [R] can R be run without installation on to a computer

@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC

Re: [R] Bioconductor package on linux machine

__ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical

Re: [R] t.test question

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI

Re: [R] how-to: installing R on Knoppix

charles loboz wrote: Installing R on Knoppix Have you looked at Quantian? I think it would have saved you lots of time. Best, Jim -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive Ann Arbor MI 48109 734-647-5623

Re: [R] mva.pairs

, Vijay [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- James W. MacDonald

Re: [R] What made us so popular Nov 16-20?

to convert the data into a simple two-column table. Figure 2 shows a snippet of the start of the file. 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] How can I put the object name in list

, Muhammad Subianto __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- James W. MacDonald University of Michigan Affymetrix and cDNA

Re: [R] Memory allocation

this limitation? -- 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-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman

Re: [R] memory issues with large data set

://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive Ann Arbor MI 48109 734-647-5623

Re: [R] red-black-green color palette?

?maPalette in the marray package of Bioconductor. HTH, Jim Thanks, Jake __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- James W

Re: [R] Power set

regression) Best, Jim -- James W. MacDonald Affymetrix and cDNA Microarray Facility University of Michigan Comprehensive Cancer Center 1500 E. Medical Center Drive Ann Arbor MI 48109 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman

Re: [R] error with the function GOHyperG from GOstats package

]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E

Re: [R] shading in line plots

that my reactions are colored by living in the US with Bush et al. running the show, but my first reaction when I see a document put out by a government that states 'we haven't threatened anyone' several times makes me wonder who they have been threatening... -- James W. MacDonald Affymetrix

Re: [R] Log(2) values to log(10) values

/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 __ [EMAIL

Re: [R] Simple plot() question

-guide.html -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

[R] Question about version argument of require() and library()

(package, character.only = TRUE, logical = TRUE, warn.conflicts = warn.conflicts, TIA, 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 __ [EMAIL

Re: [R] Question about version argument of require() and library()

() for binary packages. Thanks for the help. Best, Jim We have rather little documentation on versioned installs. -- 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] tree version 1.0-16

-project.org/posting-guide.html -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r

Re: [R] memory problem under windows

=2000M, which seems to work better for me. 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 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch

Re: [R] selecting unique columns of a matrix/data frame

. A small section of the data frame is given below. Thanks for helping. Stephen. ?unique -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 __ [EMAIL