I am working with about 600 nodes in an Rgraphviz graph. Within this graph
there are, when plotted, about 8 obvious clusters that are highly connected
within them but do not share connections between them. I have a wrapper
function that handles a lot of tasks automatically for me like setting
I need to write a table that can be opened in Excel or OpenOffice such that
there are newlines embedded within cells.
After much Googling and futzing, I can't figure out how to do this. The way
to do this within Excel is alt-Enter and I've tried '/n', '/n/r', '/r/n' per
some web suggestions
Of William Dunlap
Sent: Wednesday, October 20, 2010 10:47 AM
To: Duncan Murdoch; Mark Kimpel
Cc: r-help@r-project.org
Subject: Re: [R] ascii or regex code for alt-enter for Excel
I think Excel wants a \n for newlines
in a text cell entry but \r\n to separate
rows of a csv file. You may
I need to compare gene expression differences between multiple line pairs of
alcohol preferring and non-preferring rat lines. I have 5 such line pairs, 3
are unrelated but two were derived independently from the same parent stock.
For each line, there are 10 samples. I'll be testing multiple
Is it possible to vectorize anova over the output of a vectorized lm? I
have a gene expression matrix with each row being a gene and columns for
samples. There are several factors with interactions. I can get p values by
looping over the matrix with lm and anova, but I would like to make this as
/newsletter/issues/scgn-18-1.pdf.
If you just want to do it, see the examples in
http://had.co.nz/plyr/plyr-intro-090510.pdf.
Hadley
On Sun, Mar 7, 2010 at 7:03 PM, Mark Kimpel mwkim...@gmail.com wrote:
Is it possible to vectorize anova over the output of a vectorized lm? I
have a gene
something wrong? Following is my gcc
version and sessionInfo().
Thanks, Mark
kimpel-desktop ~/my_C: gcc --version
gcc (Ubuntu 4.4.1-4ubuntu8) 4.4.1
Copyright (C) 2009 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even
I'm having trouble using split on a very large data-set with ~1400 levels of
the factor to be split. Unfortunately, I can't reproduce it with the simple
self-contained example below. As you can see, splitting the artificial
dataframe of size ~13MB results in a split dataframe of ~ 144MB, with an
...@tajo.ucsd.eduwrote:
On Tue, 8 Dec 2009, Mark Kimpel wrote:
I'm having trouble using split on a very large data-set with ~1400 levels
of
the factor to be split. Unfortunately, I can't reproduce it with the
simple
self-contained example below. As you can see, splitting the artificial
for this case you might find
characters are faster and more space efficient.
Alternatively, you can have a look at the plyr package which uses some
tricks to keep memory usage down.
Hadley
On Tue, Dec 8, 2009 at 9:46 PM, Mark Kimpel mwkim...@gmail.com wrote:
Charles, I suspect your are correct
(317) 399-1219 Skype No Voicemail please
On Tue, Dec 8, 2009 at 11:00 PM, jim holtman jholt...@gmail.com wrote:
Also instead of 'splitting' the data frame, I split the indices and then
use those to access the information in the original dataframe.
On Tue, Dec 8, 2009 at 9:54 PM, Mark Kimpel
...@logic.at wrote:
On Thu, Nov 12, 2009 at 11:29:50AM -0500, Mark Kimpel wrote:
I am using code that previously worked to remove stopwords using package
tm.
Thanks for reporting. This is a bug in the removeWords() function in
tm version 0.5-1 available from CRAN:
require(tm)
myDocument - c
:* Mark Kimpel [mailto:mwkim...@gmail.com]
*Sent:* Thursday, November 12, 2009 11:30 AM
*To:* r-help@r-project.org; feine...@logic.at; Sam Thomas
*Subject:* package tm fails to remove the with remove stopwords
I am using code that previously worked to remove stopwords using package
tm. Even
I am using code that previously worked to remove stopwords using package
tm. Even manually adding the to the list does not work to remove the.
This package has undergone extensive redevelopment with changes to the
function syntax, so perhaps I am just missing something.
Please see my simple
I am analyzing an experiment in which time is a factor, represented by
numbers indicating time since last treatment, but in this particular case
there is no reason to think that time has a numeric meaning in the sense
that 24 would be greater than 6. We have no idea which genes will be
increasing
I'm trying to use mtext to create a main title over multiple plots. Below is
a simple self-contained example and my sessionInfo (I should note I've also
tried this with R-2.8.1 with the same results). When I execute the code
chunk below, I get the plots, but no title. I've tried this using the
(0,0,2,0))
for (i in 1:4) plot(0:1,0:1)
mtext(text = my test plots, side = 3, outer = TRUE)
Mark Kimpel wrote:
I'm trying to use mtext to create a main title over multiple plots. Below
is
a simple self-contained example and my sessionInfo (I should note I've
also
tried this with R-2.8.1
I have a vector of gene symbols, some of which have multiple aliases. In the
case of an alias, they are separated by ' \\\ '.
Here is a real world example, which would represent one element of my
vector:
Eif4g2 /// Eif4g2-ps1 /// LOC678831
What I would like to do is input the vector into a
(a, .*\\.* )
On Thu, Aug 27, 2009 at 10:03 PM, Mark Kimpel mwkim...@gmail.com wrote:
I have a vector of gene symbols, some of which have multiple aliases. In
the
case of an alias, they are separated by ' \\\ '.
Here is a real world example, which would represent one element of my
vector:
Eif4g2
I'm having trouble achieving the results I want using a regular expression.
I want to eliminate all characters that fall within square brackets as well
as the brackets themselves, returning an . I'm not sure if it's R's use of
double slash escapes or something else that is tripping me up. If I
. -- B.
F. Skinner
**
On Thu, Aug 20, 2009 at 11:39 AM, William Dunlap wdun...@tibco.com wrote:
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Mark Kimpel
Sent
.
- Phil
On Thu, 20 Aug 2009, Mark Kimpel wrote:
Well, I guess I'm not quite there yet. What I gave earlier was a
simplified
example, and did not accurately reflect the complexity of the task.
This is my real world example. As you can see, what I need to do is delete
an arbitrary number
I am familiar with packages that read and write Excel files on both Windows
and Linux platforms.
Do any packages provide similar functionality for MS Word files? I have a
lot of text processing to do and the text is embedded in ~200 different Word
files (.doc format Office 2003). All I need to do
**
On Tue, Aug 18, 2009 at 10:56 AM, Ingo Feinerer feine...@logic.at wrote:
On Tue, Aug 18, 2009 at 12:00:07PM +0200, Mark Kimpel wrote:
I am familiar with packages that read and write Excel files on both
Windows
and Linux platforms.
Do any packages provide similar functionality
problem is not whether machines think but whether men do. -- B.
F. Skinner
**
On Thu, Aug 13, 2009 at 6:11 PM, Ingo Feinerer feine...@logic.at wrote:
On Thu, Aug 13, 2009 at 03:36:22PM -0400, Mark Kimpel wrote:
I am using
I am using the package tm for text-mining of abstracts and would like to
use it to find instances of gene names that may contain white space. For
instance gene regulatory protein 1. The default behavior of tm is to parse
this into 4 separate words, but I would like to use the class constructor
I have written a wrapper for heatmap.2 called
heatmap.w.row.and.col.clust which auto-generates breaks using
breaks-round((c(seq(from=(-20 * stddev), to=(20 * stddev/20,
digits = 2) #(stddev in this case = 2.5)
This has always worked well in the past but now I am getting an error
that
Never mind, the problem seems to be that I have ignored the warning
Using scale=row or scale=column when breaks arespecified can
produce unpredictable results.Please consider using only one or the
other.
I just stop specifying the breaks and it works fine.
Mark
Having difficulties getting rJava to install on my Debian Squeeze box.
Perused the R-help list and tried some things that have worked for
others but not for me. Below is the output of my attempted build, R
CMD javareconf -e, and sessionInfo(). Note I tried the R CMD
javareconf also as root,
Switching to Sun definitely did not help, still no build with rJava,
below is the output of R CMD javareconf.
mkimpel-m90 /home/mkimpel/bin# ./R CMD javareconf
*** JAVA_HOME is not a valid path, ignoring
Java interpreter : /usr/bin/java
Java version : 1.6.0_14
Java home path :
I am using grep to locate colnames to automate a report build and have
run into a problem when a colname is not found. The use of integer(0)
in a conditional statement seems to be a no no as it has length 0.
Below is a self-contained trivial example. I would like to get
something like NA or -1 for
VoiceMail
The real problem is not whether machines think but whether men do.
-- B. F. Skinner
**
On Sat, Jul 4, 2009 at 2:47 PM, Allan Engelhardtall...@cybaea.com wrote:
On 04/07/09 18:56, Mark Kimpel wrote:
I am using grep to locate
I'm using R to do some file processing in Linux and am trying to read
in the output of find . -type f -print
~/Music_Archives_search_problem/ls.output.find.txt
This command yields a text file with each line representing the full
path name of all files in the directory and subdirs. Unfortunately,
- x + 12
nonsense
y
}
my.func(14)
Error in my.func(14) : object nonsense not found
Enter a frame number, or 0 to exit
1: my.func(14)
Selection:
On May 30, 2009, at 10:24 PM, Mark Kimpel wrote:
Duncan,
I've pared down my .Rprofile so that it has just the options line, started
**
On Sat, May 30, 2009 at 5:44 AM, Duncan Murdoch murd...@stats.uwo.cawrote:
[Sent this before completing my last sentence; here's another attempt]
On 29/05/2009 11:45 PM, Mark Kimpel wrote:
For years I have been using options(error = recover) either
For years I have been using options(error = recover) either in .Rprofile or
from within R for debugging purposes. The functionality of this appears to
have changed and I can't recover it (no pun intended) using the ?options
help page. How can I get the old functionality back, particularly from
I found the article the Y of R in the latest R news to be very
interesting. It is certainly challenging me to learn more about how R works
under the hood as the author states. What is less clear to me is whether
this approach is primarily for teaching purposes or has a real world
application. What
I'm having trouble with a Bioconductor package, an variable expected in an
environment does not seem to be there. As part of my investigation of the
problem (most likely on my end) I'd like to list the variables contained in
an environment. If you have an environment loaded, lets call it pkgEnv',
Work, Mobile VoiceMail
(317) 399-1219 Home
Skype: mkimpel
The real problem is not whether machines think but whether men do. -- B.
F. Skinner
**
On Fri, Oct 17, 2008 at 11:03 AM, Mark Kimpel [EMAIL PROTECTED] wrote:
I'm having
Subject pretty much says it all. Wonder if there is there is some code in
XML that the new gcc doesn't like? See output below:
* Installing *source* package 'XML' ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
:57PM -0400, Mark Kimpel wrote:
Subject pretty much says it all. Wonder if there is there is some code in
XML that the new gcc doesn't like? See output below:
You are wondering wronly.
* Installing *source* package 'XML' ...
checking for gcc... gcc
checking for C compiler default output
I am performing many permutations on a data-set with each permutation
producing a variable number of results. I thought that the best way to keep
track of all this in one object would be with a list ('res.lst'). To address
these variable results for each permutation I attempted to construct this
I have a large matrix, each row of which needs lm applied. I am certain than
I read an article in R-news about this within the last year or two that
discussed the application of lm to matrices but I'll be darned if I can find
it with Google. Probably using the wrong search terms.
Can someone
**
On Sun, Oct 5, 2008 at 10:28 AM, Duncan Murdoch [EMAIL PROTECTED]wrote:
On 05/10/2008 10:08 AM, Mark Kimpel wrote:
I have a large matrix, each row of which needs lm applied. I am certain
than
I read an article in R-news about this within
I'm making some plots on the same page and would like to include an overall
title instead of individual main titles as they are similar and their x and
y axis labels are sufficient to distinguish them.
Is there a way to assign an overall main to this page of plots?
Mark
--
Mark W. Kimpel MD **
Ouch! I had searched the archives and read over ?par and ?plot, but sure
missed the post of today. Thanks, Mark
On Tue, Aug 5, 2008 at 7:27 PM, Marc Schwartz [EMAIL PROTECTED]wrote:
on 08/05/2008 06:05 PM Mark Kimpel wrote:
I'm making some plots on the same page and would like to include
/2008 12:54 PM Mark Kimpel wrote:
I'm running R on Linux and use emacs as my editor. When doing
edit(vignette(foo.vignette)) I would like to invoke emacs rather than
the
default vi. I am able to manually set this by editing $R_HOME/etc/Renviron
but would like to avoid doing this with each install
Where is the link on www.r-project.org or CRAN to download source code for
development versions of packages? This is straightforward for BioConductor
packages but I can't seem to find it for R packages.
Mark
--
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University
and input. Ben, if you get such a list of packages
with functions that depend on rgl, send it to me.
Mark
On Thu, Jun 26, 2008 at 7:02 AM, Duncan Murdoch [EMAIL PROTECTED] wrote:
Mark Kimpel wrote:
Thanks for the pointers. I think the package is great, just want to
use it to its full potential without
:
[1] rgl_0.79 graph_1.18.1
loaded via a namespace (and not attached):
[1] cluster_1.11.11 tools_2.7.1
On Wed, Jun 25, 2008 at 5:25 PM, Duncan Murdoch [EMAIL PROTECTED] wrote:
Mark Kimpel wrote:
Ben and Duncan,
Thanks for your helpful suggestions. Im having some difficulty
navigating
I'd like to use rgl.surface (or some other function if more
appropriate) to create a horizontal and vertical transparent grey
slice (plane) running through both the x and y origins and extending
across the z axis, i.e. the 3-d equivalent of the normal 2-d
coordinate axes we are all familiar with.
this helps,
- Stu
On May 6, 12:52 pm, Mark Kimpel [EMAIL PROTECTED] wrote:
Subject pretty much says it all. I am running 64-bit Ubuntu 8.04, i.e. Hardy
Heron, have openmpi installed, and get the following error message with
attempted install of Rmpi. sessionInfo() follows.
Mark
checking for ANSI
(1:nc %% 2))
par(mfrow=c(2,1))
hist(rt1$p.value, breaks=100, col=mistyrose)
hist(rt2$p.value, breaks=100, col=mistyrose)
--
Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
Mark Kimpel a écrit 07/06/2008 18
I'm working with a genomic data-set with ~31k end-points and have
performed an F-test across 5 groups for each end-point. The QA
measurments on the individual micro-arrays all look good. One of the
first things I do in my work-flow is take a look at the p-valued
distribution. it is my
not in this case.
Ubuntu currently is distributing graphviz 2.16.1
Thanks,
Mark
On Wed, May 7, 2008 at 12:14 AM, Michael Lawrence [EMAIL PROTECTED]
wrote:
On Tue, May 6, 2008 at 6:06 PM, Mark Kimpel [EMAIL PROTECTED] wrote:
R crashed just after the warnings were issued, but ggobi kept running
Uninstalling and reinstalling ggobi via Synaptic solved the problem, at
least for the demo data mtcars. Rotation works fine. No crashes on exit.
Thanks for the good advice.
Mark
On Wed, May 7, 2008 at 2:12 PM, Paul Johnson [EMAIL PROTECTED] wrote:
On Tue, May 6, 2008 at 12:32 PM, Mark Kimpel
Subject pretty much says it all. I am running 64-bit Ubuntu 8.04, i.e. Hardy
Heron, have openmpi installed, and get the following error message with
attempted install of Rmpi. sessionInfo() follows.
Mark
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for
I am running 64-bit Ubuntu 8.04 and when I invoke rggobi the interactive
graph displays but R crashes. See my sessionInfo() and a short example
below. Ggobi and rggobi installed without complaints. Mark
sessionInfo()
R version 2.7.0 Patched (2008-05-04 r45620)
x86_64-unknown-linux-gnu
locale:
, and perhaps a sane
system would not compile it. Try
% chmod -x RCurl/src/curl_base64.c
and then
% R CMD INSTALL RCurl
Martin
Mark Kimpel [EMAIL PROTECTED] writes:
I'm having same problem on Ubuntu 64-bit Hardy Heron. A bunch of
security
patches from Ubuntu came out and I installed
- one for
the old and one for the new and the configuration will endeavor to
determine which is appropriate.
~ HTH
~ D.
Mark Kimpel wrote:
| Martin,
|
| Well, thanks for jumping in! We need all the help we can get ;)
|
| I changed the execute bit as you suggested and recompiled
I would like to create a 3d scatterplot that is interactive in the sense
that I can spin it on its axes to better visualize some PCA results I have.
What are the options in R? I've looked at RGL and perhaps it will suffice
but it wasn't apparent from the documentation I found.
Any demo scripts
Can merge be tricked into merging via rownames as opposed to via contents of
a particular column? I have two data.frames with overlapping, but out of
order, rownames, but no column contents in common and would like to merge
without cbinding the rownames to the data.frames.
Mark
--
Mark W. Kimpel
As a medical researcher, I keep tabs on the journals Bioinformatics andd BMC
Bioinformatics. If your package is for 'omics, those are good journals to
look at.
Mark
On Sun, Mar 30, 2008 at 10:02 AM, Peter Dalgaard [EMAIL PROTECTED]
wrote:
Gavin Simpson wrote:
On Sun, 2008-03-30 at 15:01
I'll throw one more idea into the mix. I agree with Bill that a rating
system for respondents is probably not that practical and of not the highest
importance. It also seems like a recipe for creating inter-personal problems
that the list doesn't need.
I do like Bill's idea of a review system for
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