[R] Font Path question

2014-02-11 Thread James W. MacDonald
methods base Any suggestions 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

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

2013-12-09 Thread James W. MacDonald
biology.informatics.conductor -- 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 https://stat.ethz.ch/mail

Re: [R] limma contrast matrix

2011-08-04 Thread James W. MacDonald
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] help required for GO Annotation problem

2011-06-28 Thread James W. MacDonald
/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] replace non numeric with "NA"

2011-04-29 Thread James W. MacDonald
tp://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] repeat write.table with the same code many times

2010-11-30 Thread James W. MacDonald
g else to the file at that point. You could also use writeLines(), but that is likely too low-level for your needs. Best, Jim Thanks, Laura [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEA

Re: [R] Problems in running affylmGUI

2010-11-29 Thread James W. MacDonald
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 day, and s

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

2010-06-28 Thread James W. MacDonald
e. __ 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. _________

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

2010-06-24 Thread James W. MacDonald
d to allow one to query any DBMS. Since RMySQL is MySQL-specific, it may be more efficient. 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 wrote: Hi Ralf, Ralf B wrote: I am running a simple SQL SELECT statemen

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

2010-06-23 Thread James W. MacDonald
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 of Mich

Re: [R] xtable with Sweave

2010-06-14 Thread James W. MacDonald
ne: 3371-4346 __ 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

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

2010-02-08 Thread James W. MacDonald
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 interna

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

2010-02-03 Thread James W. MacDonald
hz.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 De

Re: [R] what "~1"stands for?

2010-01-22 Thread James W. MacDonald
SE 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 Arbor MI 4810

Re: [R] R package dependencies

2010-01-14 Thread James W. MacDonald
-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?

2009-12-07 Thread James W. MacDonald
tp://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] Replying to Posts Within Same Thread

2009-12-02 Thread James W. MacDonald
ect you already 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 ** Elec

Re: [R] Importing tRNA data into R ?

2009-11-18 Thread James W. MacDonald
-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] Incremental ReadLines

2009-11-02 Thread James W. MacDonald
-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] R 2.10 under Windows XP: glitches and successes

2009-10-29 Thread James W. MacDonald
posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ 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 c

Re: [R] Basic Sweave

2009-10-27 Thread James W. MacDonald
message was sent on behalf of alexander.weids...@gmail.com at openSubscriber.com http://www.opensubscriber.com/messages/r-help@r-project.org/topic.html __ 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/p

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

2009-10-27 Thread James W. MacDonald
version deleted]] __ 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. Biostatistic

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

2009-10-23 Thread James W. MacDonald
00 44 comps 45 comps 46 comps 47 comps 48 comps 49 comps 50 comps X100 100 100 100 100 100 100 octane 100 100 100 100 100 100 100 51 comps 52 comps 53 comps X100 100 10

Re: [R] predict missing values with svm

2009-09-28 Thread James W. MacDonald
ct.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 Department of Human

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

2009-09-14 Thread James W. MacDonald
at this row.names vector is 2. 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

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

2009-08-10 Thread James W. MacDonald
iling 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 of Human

Re: [R] calculating median with a condition

2009-07-20 Thread James W. MacDonald
ML version deleted]] __ 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. Biost

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

2009-07-09 Thread James W. MacDonald
Rowv=rowv, Colv=colv) Best, Jim Many thanks, Chrysanthi. 2009/7/8 James W. MacDonald <mailto:jmac...@med.umich.edu>> Hi Chrysanthi, Chrysanthi A. wrote: Hi, I am analysing gene expression data using the heatmap.2 function in R and I

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

2009-07-08 Thread James W. MacDonald
tps://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 of Human Gen

Re: [R] question about package biomaRt

2009-06-23 Thread James W. MacDonald
, 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 mai

Re: [R] specify the number of decimal numbers

2009-05-14 Thread James W. MacDonald
more 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 73

Re: [R] specify the number of decimal numbers

2009-05-14 Thread James W. MacDonald
e 'print sprintf("%.1f", 0.15) . "\n";' 0.1 vQ __ 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-contain

Re: [R] rbind help

2009-05-12 Thread James W. MacDonald
s mike -- 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/mailm

Re: [R] unloading loaded packages

2009-04-30 Thread James W. MacDonald
producible 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://stat.ethz.ch/mai

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

2009-04-07 Thread James W. MacDonald
d i dont want the dendogram. I am using the R version 2.8.0 (2008-10-20)". Thanks, Tanuja [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-

Re: [R] Programming objects in R

2009-04-02 Thread James W. MacDonald
osting-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 __ R-help@r-project.org mailing list https://stat

Re: [R] PLS package loading error!

2009-03-30 Thread James W. MacDonald
valide -- a-t-il été installé < 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

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

2009-03-17 Thread James W. MacDonald
_ 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

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

2008-11-03 Thread James W. MacDonald
r_1.16.0 survival_2.34 annotate_1.16.1 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.

Re: [R] Opening a web browser from R?

2008-08-15 Thread James W. MacDonald
rom within R. I was looking at the help for 'url' and I can see I can probably access the information I need and display it in my own way, but can I somehow just open the given url with my web browser of choice? many thanks for any help, Jose -- James W. MacDonald, M.S. Biostat

Re: [R] heatmap.2 dendogram algorithm

2008-06-17 Thread James W. MacDonald
gives me Usage: 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 Univ

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

2008-06-13 Thread James W. MacDonald
Germany __ 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. Mac

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

2008-05-16 Thread James W. MacDonald
he clustering every time is not feasible. Thanks, 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-co

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

2008-05-15 Thread James W. MacDonald
ling 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 of Michiga

Re: [R] RODBC / odbcConnectExcel Issue

2008-04-04 Thread James W. MacDonald
t; You want your table name to be wrapped in []. In this case the query should be SELECT * FROM [nameclass$] Best, Jim > > [[alternative HTML version deleted]] > > __ > R-help@r-project.org mailing list > https://stat.eth

Re: [R] Newbie help with Sweave

2008-03-25 Thread James W. MacDonald
====== >> \documentclass[a4paper]{article} >> >> \title{Sweave Example 1} >> \author{Friedrich Leisch} >> >> \begin{document} >> >> \maketitle >> >> In this example we embed parts of the examples from the >> \

Re: [R] Installation of R, Sweave, ESS and [X]Emacs on Windows?

2008-03-20 Thread James W. MacDonald
@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 Mi

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

2008-03-03 Thread James W. MacDonald
gt;> I am pretty new to R. I think it is showing me the entire p-value. >> >> >> >> -- >> View this message in context: >> http://www.nabble.com/Calculating-the-t-test-for-each-row-tp15808716p15808716.html >> Sent from the R help mailing list archive at Nabble.com. >> &g

Re: [R] problem with creation of eSet

2008-02-28 Thread James W. MacDonald
t; ExpressionSet) instead > > > > > > Can someone suggest me how to use the new method AnnotatedDataFrame to create > eSet? > > > > > > Thanks > > > > Manisha > > > > > > > [[alternative HTML version deleted]] > > _

Re: [R] select repositories under linux

2008-01-22 Thread James W. MacDonald
n unix. Does anyone have any idea on this? >> >> Thank you in advance, >> Eleni >> >> [[alternative HTML version deleted]] >> >> __ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/li

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

2008-01-21 Thread James W. MacDonald
on halted > > I do have pdflatex, it's what I use all of the time. However, how do I > point to it for this build process? > >> -Original Message- >> From: James W. MacDonald [mailto:[EMAIL PROTECTED] >> Sent: Monday, January 21, 2008 4:09 PM >> To: Dor

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

2008-01-21 Thread James W. MacDonald
rg 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 Microarr

Re: [R] R and samr under Linux

2008-01-21 Thread James W. MacDonald
>> 3. Does R language have a way for me to define which processor in a >> cluster >> I would >> >> like to execute a section of code upon, like in MPI? >> >> >> >> Please let me know some of these things, if you can help. >> >> Than

Re: [R] Scatterplot Showing All Points

2007-12-18 Thread James W. MacDonald
and all required dependencies. Best, Jim > > Duncan 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 __

Re: [R] Scatterplot Showing All Points

2007-12-18 Thread James W. MacDonald
_ > 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. --

Re: [R] hclust in heatmap.2

2007-12-06 Thread James W. MacDonald
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 count the number of sequences in matrix?

2007-11-13 Thread James W. MacDonald
table(textConnection(x), header=TRUE) > x > > Any idea how to do this in R? > > Best regards, > Lauri > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the postin

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

2007-11-12 Thread James W. MacDonald
0/lib/R/library > Please check your permissions or provide a different 'lib' parameter. > Execution halted > > Any pointers? > -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Driv

Re: [R] please help me

2007-11-08 Thread James W. MacDonald
start = list(c0 = 0, > : > number of iterations exceeded maximum of 50 > best regards. > Sadeghian. > > __ > > > > [[alternative HTML version deleted]] > > _____

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

2007-10-10 Thread James W. MacDonald
ion has length > 1 and only the first element will be used > 8: In if (x < 0) a <- -1 else a <- 1 : > the condition has length > 1 and only the first element will be used > > [[alternative HTML version deleted]] > > __