Re: [ESS] emacs theme for polymode with noweb files

I personally like Dracula mode, although Nord seems pretty nice as well. -Original Message- From: ESS-help On Behalf Of LaurentEss via ESS-help Sent: Sunday, December 3, 2023 5:48 PM To: ess-help@r-project.org Subject: [ESS] emacs theme for polymode with noweb files Dear ESS-list,    

Re: [ESS] knitr tutorial for ESS

Vincent Goulet has an installer that sets everything up for you, that you can get here. https://vigou3.github.io/emacs-modified-windows/ It does all the syntax highlighting, plus has polymode support which is nice for Rmd files. I can't help with any key combinations to build output. I just set

[R] Font Path question

as to how I might track this down? Best, Jim -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 __ R-help@r-project.org mailing list

Re: [R] [BioC] Why daisy() in cluster library failed to exclude NA when computing dissimilarity

W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] limma contrast matrix

-contained, reproducible code. -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ** Electronic Mail is not secure

Re: [R] help required for GO Annotation problem

, self-contained, reproducible code. -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ** Electronic Mail

Re: [R] replace non numeric with NA

, reproducible code. -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ** Electronic Mail is not secure, may not be read every

Re: [R] repeat write.table with the same code many times

-project.org 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 Douglas Lab University of Michigan

Re: [R] Problems in running affylmGUI

. -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ** Electronic Mail is not secure, may not be read every day, and should

Re: [R] Popularity of R, SAS, SPSS, Stata...

. __ R-help@r-project.org 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 Douglas Lab University

Re: [R] RJDBC vs RMySQL vs ???

. Anyway, why don't you just try it and see? Best, Jim Best, Ralf On Wed, Jun 23, 2010 at 4:36 PM, James W. MacDonald jmac...@med.umich.edu wrote: Hi Ralf, Ralf B wrote: I am running a simple SQL SELECT statement that involvs 50k + data points using R and the RJDBC interface. I am facing

Re: [R] RJDBC vs RMySQL vs ???

http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826

Re: [R] xtable with Sweave

__ R-help@r-project.org 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 Douglas Lab University

Re: [R] [BioC] objects masked from packages

Hi Assa, First off, please don't cross-post. This is really an R-help question, as it is about the R language rather than a specific BioC package. Assa Yeroslaviz wrote: dear all, I have a problem with a masked object in a package we created here. we make a package for a workflow of

Re: [R] typo in contrast package's vignettes

/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 Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St

Re: [R] what ~1stands for?

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 Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615

Re: [R] R package dependencies

-project.org 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 Douglas Lab University of Michigan

Re: [R] savePlot for Mac and / or Linux?

, self-contained, reproducible code. -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ** Electronic Mail is not secure

Re: [R] Replying to Posts Within Same Thread

know): https://stat.ethz.ch/pipermail/r-help/ Best -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826

Re: [R] Importing tRNA data into R ?

commented, minimal, self-contained, reproducible code. -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 __ R-help@r-project.org

Re: [R] Incremental ReadLines

commented, minimal, self-contained, reproducible code. -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 __ R-help@r-project.org

Re: [R] R 2.10 under Windows XP: glitches and successes

-help@r-project.org 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 Douglas Lab University of Michigan

Re: [R] if there is a package can do blast for gene in R?

]] __ R-help@r-project.org 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 Douglas Lab

Re: [R] Basic Sweave

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 Douglas Lab University of Michigan Department

Re: [R] data frame is killing me! help

100 octane 100 100 100 100 100 100 100 51 comps 52 comps 53 comps X100 100 100 octane 100 100 100 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human

Re: [R] predict missing values with svm

/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 Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E

Re: [R] Eliminate cases in a subset of a dataframe

. How I can refer to cases after creating a subset (e.g., in order to exclude them). Many thanks in advance, Best, Holger -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826

Re: [R] Need Advice: Considering Converting a Package from S3 to S4

/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 Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann

Re: [R] calculating median with a condition

]] __ R-help@r-project.org 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 Douglas Lab

Re: [R] heatmap.2: question regarding the raw z-score

http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St

Re: [R] heatmap.2: question regarding the raw z-score

-contained, reproducible code. -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 __ R-help@r-project.org mailing list https

Re: [R] question about package biomaRt

-contained, reproducible code. -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 __ R-help@r-project.org mailing list https

Re: [R] specify the number of decimal numbers

__ R-help@r-project.org 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 Douglas Lab

Re: [R] specify the number of decimal numbers

personal nature, so I'll let you get back to tilting at windmills. vQ -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826

Re: [R] rbind help

=180])) I would do the conversion in place: striae$orientation - ifelse(striae$orientation 108, striae$orientation - 180, striae$orientation) Best, Jim Not being a regular R user I suspect the syntax is easy when you know it!! Any help much appreciated. Best wishes mike -- James W

Re: [R] unloading loaded packages

. -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r

Re: [R] heatmap.2 no reordering of the columns and rows

]] __ R-help@r-project.org 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 Douglas Lab University

Re: [R] Programming objects in R

, reproducible code. -- James W. MacDonald, M.S. Biostatistician Douglas Lab 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

Re: [R] PLS package loading error!

2.0.0 ? Could you please help me to solve this problem? Regards Damien -- James W. MacDonald, M.S. Biostatistician Douglas Lab 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 __ R-help@r-project.org mailing list https

Re: [R] Need to build package for Affy HT HG-U133+ PM arrays

/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 Douglas Lab 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826

Re: [R] Help with 'annotation' in GOHyperGParamsClass

xtable_1.5-2 [16] AnnotationDbi_1.0.6 RSQLite_0.6-4 DBI_0.2-4 graph_1.16.1Biobase_1.16.3 [21] GO_2.0.1 loaded via a namespace (and not attached): [1] KernSmooth_2.22-22 RColorBrewer_1.0-2 cluster_1.11.9 grid_2.6.2 -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D

Re: [R] heatmap.2 dendogram algorithm

: hclust(d, method = complete, members=NULL) Thank you and sorry if I posted this in the wrong place. If I have, please let me know and I will move it to the appropriate list. -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer

Re: [R] Problem with Freq function {prettyR}

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 7410 CCGC Ann

Re: [R] heatmap on pre-established hclust output?

, Joh __ R-help@r-project.org 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

Re: [R] Heatmap.2 - eliminate cluster and dendrogram

://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

Re: [R] RODBC / odbcConnectExcel Issue

]] __ R-help@r-project.org 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

Re: [R] Newbie help with Sweave

=FALSE= boxplot(Ozone ~ Month, data = airquality) @ \end{center} \end{document} -- 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] Installation of R, Sweave, ESS and [X]Emacs on Windows?

-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 MI 48109 734-647-5623

Re: [R] Calculating the t-test for each row

-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] problem with creation of eSet

-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 7410

Re: [R] select repositories under linux

]] __ R-help@r-project.org 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] R and samr under Linux

-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 MI 48109 734-647-5623

Re: [R] Adding an Sweave Vignette to a package

__ R-help@r-project.org 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

Re: [R] Adding an Sweave Vignette to a package

: James W. MacDonald [mailto:[EMAIL PROTECTED] Sent: Monday, January 21, 2008 4:09 PM To: Doran, Harold Cc: R Help Subject: Re: [R] Adding an Sweave Vignette to a package Hi Harold, Doran, Harold wrote: I'm finalizing development of a package that will include a vignette. Without

Re: [R] Scatterplot Showing All Points

, 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 __ R-help@r-project.org

Re: [R] Scatterplot Showing All Points

Murdoch -- 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@r-project.org mailing list https://stat.ethz.ch

Re: [R] hclust in heatmap.2

. -- 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@r-project.org mailing list https://stat.ethz.ch/mailman

Re: [R] How to count the number of sequences in matrix?

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 MI 48109 734-647-5623

Re: [R] How to set up your library location for multiple users

halted Any pointers? -- 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@r-project.org mailing list

Re: [R] please help me

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 University

Re: [R] simple function with if - lapply to dataframe

-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 __ R-help@r-project.org mailing list