[R] Need Help: Installing/Using xtable package
Hi all, Let me know if I need to ask this question of the bioconductor group. I used the bioconductor utility to install this package and also the CRAN package.install function. My computer crashed a week ago. Today I reinstalled all my bioconductor/R packages. One of my scripts is giving me the following error: in my script I set: library(xtable) print.xtable( and receive this error: Error : could not find function print.xtable This is a new error and I cannot find the source. I reinstalled xtable with the messages below(which are the same whether I use CRAN or bioconductor): Any help is appreciated! Thanks! Matt biocLite(xtable) Running biocinstall version 2.0.8 with R version 2.5.1 Your version of R requires version 2.0 of Bioconductor. Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependenc ies, : argument 'lib' is missing: using '/home/mdj/R/i486-pc-linux-gnu-library /2.5' trying URL 'http://cran.fhcrc.org/src/contrib/xtable_1.5-1.tar.gz' Content type 'application/x-gzip' length 134758 bytes opened URL == downloaded 131Kb * Installing *source* package 'xtable' ... ** R ** data ** inst ** preparing package for lazy loading ** help Building/Updating help pages for package 'xtable' Formats: text html latex example print.xtable texthtmllatex stringtexthtmllatex table.attributes texthtmllatex tli texthtmllatex xtabletexthtmllatex example ** building package indices ... * DONE (xtable) The downloaded packages are in /tmp/RtmpGThCuI/downloaded_packages __ 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.
Re: [R] Need Help: Installing/Using xtable package
Ok, I got it now. Just: print(xtable(...),) Thanks! Matt On 8/9/07, Seth Falcon [EMAIL PROTECTED] wrote: Peter Dalgaard [EMAIL PROTECTED] writes: M. Jankowski wrote: Hi all, Let me know if I need to ask this question of the bioconductor group. I used the bioconductor utility to install this package and also the CRAN package.install function. My computer crashed a week ago. Today I reinstalled all my bioconductor/R packages. One of my scripts is giving me the following error: in my script I set: library(xtable) print.xtable( and receive this error: Error : could not find function print.xtable This is a new error and I cannot find the source. Looks like the current xtable is no longer exporting its print methods. Why were you calling print.xtable explicitly in the first place? Indeed, xtable now has a namespace. The S3 methods are not exported because they should not be called directly; rather, the generic function (in this case print) should be called. The addition of the namespace is really a good. Yes, it will cause some hicups for folks who were calling the methods directory (tsk tsk). But the addition fixes breakage that was occuring due to internal xtable helper functions being masked. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center BioC: http://bioconductor.org/ Blog: http://userprimary.net/user/ __ 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.
Re: [R] Need Help: User Defined R Functions in Sweave/Latex
Back to Dieter's solution for a moment, take note of the Sweave FAQ (also in the above manual), specifically FAQ A.9, which covers the issue of figure chunks and multiple plots, proposing a looping approach consistent with Dieter's. I hope that this might give you some other insights into alternative approaches. HTH, Marc Schwartz Marc, You sure did help me. I reviewed A.9 and found that I simply needed to set: results=tex, echo=false = in the initial function call. Then the route I was pursuing worked smashingly. The rest of your post has me thinking about my approach. I have more than enough data, in my mind at least, to justify the extra effort (and possible confusion) of including captions. I'll need to look at the options for the pdf function to see if it already has the functionality I am looking for. Thank you very much for the nice reply to my post! Matt __ 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.
[R] Need Help: User Defined R Functions in Sweave/Latex
Dear all,
I want to start my post by expressing my sincere gratitude for all the
help this group has given me in Sweave/Latex/R. The tools are
excellent and so is the community!
On to the question.
My Sweave code is intended to make lots of plots and create a *.pdf
document. Sweave is perfect for this. The only problem is that I find
myself using the same R code, within my Sweave input file over an
over. I know about Latex macros and I can even get R functions,
essentially used as subroutines, to sort of work. \Sexpr{} will not
work because the R code I want to use over and over is in the R
environment. I've tried numerous ways to tackle this process and could
really use some help. If there is some easier way to do this please
let me know!
This is the R function:
basicplot - function(x, nplots, sectionname){
# Begin to make figure here
file = paste(scatter,nplots, .pdf, sep=)
pdf(file = file,paper=special, width=6, height = 6)
plot(x)
dev.off()
cat(\\begin{figure}\n)
cat(\\includegraphics{,file,}\n, sep=)
cat(\\caption{, sectionname,}\n, sep = )
cat(\\end{figure}\n)
#End figure making
}
The aim is to generate Latex code which will have some basic
information as part of the caption. The trouble seems to be that the
output from the function appears to latex as if it is protected R code
when I really want to create output that pdflatex will act on.
Essentially, the resulting *.pdf contains the lines output by the cat
function in basicplot. Or:
\begin{figure}
\includegraphics{scatter1.pdf}
\caption{myname}
\end{figure}
These lines are not in the environment acted by Latex. I tried a
variant of the function where results=tex,echo=FALSE and received
the same result. Below are the files *.Snw - *.tex - *.pdf and the
output I received while compiling. If there is anything else I can
give to help you help me just let me know. Thanks!
Matt
My system:
T41 IBM Thinkpad
Ubuntu Feisty (7.04)
R version 2.5
testmacro3.Snw:
[EMAIL PROTECTED]:~/mydocs/R$ more testmacro3.Snw
\documentclass[a4paper]{article}
\usepackage{fullpage}
echo=f=
basicplot - function(x, nplots, sectionname){
# Begin to make figure here
file = paste(scatter,nplots, .pdf, sep=)
pdf(file = file,paper=special, width=6, height = 6)
plot(x)
dev.off()
cat(\\begin{figure}\n)
cat(\\includegraphics{,file,}\n, sep=)
cat(\\caption{, sectionname,}\n, sep = )
cat(\\end{figure}\n)
#End figure making
}
@
\begin{document}
Filler text here.\\
=
library(flowCore)
x - read.FCS(/home/mdj/data/yifacs2/NL7_PHA03_1.fcs, transformation = FALSE,
alter.names = TRUE);
basicplot(x, nplots = 1, sectionname=myname)
@
End text here \\
\end{document}
testmacro3.tex
\usepackage{/usr/share/R/share/texmf/Sweave}
\begin{document}
Filler text here.\\
\begin{Schunk}
\begin{Sinput}
library(flowCore)
\end{Sinput}
\begin{Soutput}
Scalable Robust Estimators with High Breakdown Point (version 0.3-05)
\end{Soutput}
\begin{Sinput}
x - read.FCS(/home/mdj/data/yifacs2/NL7_PHA03_1.fcs, transformation = FALSE
,
+ alter.names = TRUE)
basicplot(x, nplots = 1, sectionname = myname)
\end{Sinput}
\begin{Soutput}
\begin{figure}
\includegraphics{scatter1.pdf}
\caption{myname}
\end{figure}
\end{Soutput}
\end{Schunk}
End text here \\
\end{document}
testmacro3.pdf:
Filler text here.
library(flowCore)
Scalable Robust Estimators with High Breakdown Point (version 0.3-05)
x - read.FCS(/home/mdj/data/yifacs2/NL7_PHA03_1.fcs, transformation =
FALSE,
+ alter.names = TRUE)
basicplot(x, nplots = 1, sectionname = myname)
\begin{figure}
\includegraphics{scatter1.pdf}
\caption{myname}
\end{figure}
End text here
Output:
[EMAIL PROTECTED]:~/mydocs/R$ R CMD Sweave testmacro3.Snw
[1] Welcome to my custom R eenvironment!
library(utils); Sweave(testmacro3.Snw)
Writing to file testmacro3.tex
Processing code chunks ...
1 : term verbatim
2 : echo term verbatim
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()' or start with 'help(Biobase)'. For details
on reading vignettes, see the openVignette help page.
Loading required package: rrcov
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
You can now run LaTeX on 'testmacro3.tex'
[EMAIL PROTECTED]:~/mydocs/Rpdflatex testmacro3.tex
This is pdfeTeX, Version 3.141592-1.21a-2.2 (Web2C 7.5.4)
entering extended mode
(./testmacro3.tex
LaTeX2e 2003/12/01
Babel v3.8d and hyphenation patterns for american, french, german, ngerman, b
ahasa, basque, bulgarian, catalan, croatian, czech, danish, dutch, esperanto, e
stonian, finnish, greek, icelandic, irish, italian, latin, magyar, norsk, polis
h, portuges, romanian, russian, serbian, slovak, slovene, spanish, swedish, tur
kish, ukrainian, nohyphenation, loaded.
(/usr/share/texmf-tetex/tex/latex/base/article.cls
Document Class: article 2004/02/16 v1.4f Standard LaTeX document class
(/usr/share/texmf-tetex/tex/latex/base/size10.clo))
[R] Help With Sweave:
Hi All, I am running Ubuntu Feisty (7.04) on a Thinkpad T41. I've installed the nowebm package for Ubuntu. Working from this HowTo: http://www.ci.tuwien.ac.at/~leisch/Sweave/example-1.Snw I try to compile the example *.Snw as in the Sweave manual: [EMAIL PROTECTED]:~/Desktop/Sweave/example1$ noweb example-1.Snw Can't open output file Despite the error, a *.tex file is produced. Now I am stuck because I cannot seem to get the CTAN noweb package correctly installed for my Latex installation. I guess I am somewhat spoiled by the Synaptic package manager. Here is the result of my best attempt to get the noweb package installed: Following the guidelines for installing packages found here: http://www.ctan.org/tex-archive/info/beginlatex/html/chapter5.html#pk... I try to install this package: http://tug.ctan.org/cgi-bin/ctanPackageInformation.py?id=noweb But there are no *.ins or *.dtx files. There is a *.sty though... I follow the instructions in the readme and this is the result (Here are a few of the errors, the complete output is below): make: [install-shell] Error 1 (ignored) make: [install-tex] Error 1 (ignored) make: [install-code] Error 1 (ignored) A bunch of errors. What am I doing wrong? Any help is much appreciated! Of course, if there is a better place for me to ask this question please let me know where! Thanks! Matt [EMAIL PROTECTED]:~/downloads/noweb-2.11b/src$ sudo make all install cd c; make CC=gcc -ansi -pedantic CFLAGS= all make[1]: Entering directory `/home/mdj/downloads/noweb-2.11b/src/c' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/home/mdj/downloads/noweb-2.11b/src/c' for i in shell lib xdoc tex; do (cd $i; make all); done make[1]: Entering directory `/home/mdj/downloads/noweb-2.11b/src/ shell' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/home/mdj/downloads/noweb-2.11b/src/shell' make[1]: Entering directory `/home/mdj/downloads/noweb-2.11b/src/lib' chmod +x unmarkup emptydefn toascii nwmtime pipedocs h2a btdefn make[1]: Leaving directory `/home/mdj/downloads/noweb-2.11b/src/lib' make[1]: Entering directory `/home/mdj/downloads/noweb-2.11b/src/xdoc' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/home/mdj/downloads/noweb-2.11b/src/xdoc' make[1]: Entering directory `/home/mdj/downloads/noweb-2.11b/src/tex' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/home/mdj/downloads/noweb-2.11b/src/tex' cd awk; make ICONT=icont ICONC=iconc all make[1]: Entering directory `/home/mdj/downloads/noweb-2.11b/src/awk' chmod +x noindex totex noidx tohtml make[1]: Leaving directory `/home/mdj/downloads/noweb-2.11b/src/awk' mkdir /usr/local/noweb /usr/local/noweb/lib 2/dev/null make: [install-shell] Error 1 (ignored) sed s@|LIBDIR|@/usr/local/noweb/lib@ shell/noweb /usr/local/noweb/ noweb chmod +x /usr/local/noweb/noweb sed s@|LIBDIR|@/usr/local/noweb/lib@ shell/notangle /usr/local/ noweb/notangle chmod +x /usr/local/noweb/notangle sed s@|LIBDIR|@/usr/local/noweb/lib@ shell/noweave / usr/local/noweb/noweave chmod +x /usr/local/noweb/noweave sed s@|LIBDIR|@/usr/local/noweb/lib@ shell/nountangle /usr/local/ noweb/nountangle chmod +x /usr/local/noweb/nountangle sed s@|LIBDIR|@/usr/local/noweb/lib@ shell/nodefs /usr/local/noweb/ nodefs chmod +x /usr/local/noweb/nodefs sed s@|LIBDIR|@/usr/local/noweb/lib@ shell/noroots /usr/local/ noweb/noroots chmod +x /usr/local/noweb/noroots sed s@|LIBDIR|@/usr/local/noweb/lib@ shell/nuweb2noweb /usr/local/ noweb/nuweb2noweb chmod +x /usr/local/noweb/nuweb2noweb sed s@|LIBDIR|@/usr/local/noweb/lib@ shell/cpif /usr/local/noweb/ cpif chmod +x /usr/local/noweb/cpif sed s@|LIBDIR|@/usr/local/noweb/lib@ shell/htmltoc /usr/local/ noweb/htmltoc chmod +x /usr/local/noweb/htmltoc sed s@|LIBDIR|@/usr/local/noweb/lib@ shell/noroff /usr/local/noweb/ noroff chmod +x /usr/local/noweb/noroff sed s@|LIBDIR|@/usr/local/noweb/lib@ shell/toroff /usr/local/noweb/ lib/toroff chmod +x /usr/local/noweb/lib/toroff cp shell/tmac.w /usr/local/noweb/lib mkdir /usr/local/noweb /usr/local/noweb/lib 2/dev/null make: [install-code] Error 1 (ignored) strip c/nt c/markup c/mnt c/finduses cp c/nt c/markup c/mnt c/finduses /usr/local/noweb/lib cd awk; make ICONT=icont ICONC=iconc LIB=/usr/local/noweb/lib BIN=/usr/ local/noweb install make[1]: Entering directory `/home/mdj/downloads/noweb-2.11b/src/awk' chmod +x noindex totex noidx tohtml cp totex noidx tohtml /usr/local/noweb/lib cp noindex /usr/local/noweb make[1]: Leaving directory `/home/mdj/downloads/noweb-2.11b/src/awk' cd lib; make LIB=/usr/local/noweb/lib install make[1]: Entering directory `/home/mdj/downloads/noweb-2.11b/src/lib' chmod +x unmarkup emptydefn toascii nwmtime pipedocs h2a btdefn cp unmarkup emptydefn toascii nwmtime h2a btdefn /usr/local/noweb/lib sed 's@|LIBDIR|@/usr/local/noweb/[EMAIL PROTECTED]' pipedocs /usr/local/noweb/ lib/pipedocs chmod +x /usr/local/noweb/lib/pipedocs make[1]: Leaving directory
Re: [R] Help With Sweave:
Dirk,
Your solution worked wonders! This is outstanding! Thank you!
Matt
On 6/19/07, Dirk Eddelbuettel [EMAIL PROTECTED] wrote:
Matt,
On 19 June 2007 at 21:23, M. Jankowski wrote:
| Hi All,
|
| I am running Ubuntu Feisty (7.04) on a Thinkpad T41. I've installed
| the nowebm package for Ubuntu. Working from this HowTo:
| http://www.ci.tuwien.ac.at/~leisch/Sweave/example-1.Snw
| I try to compile the example *.Snw as in the Sweave manual:
|
| [EMAIL PROTECTED]:~/Desktop/Sweave/example1$ noweb example-1.Snw
| Can't open output file
|
| Despite the error, a *.tex file is produced. Now I am stuck because I
| cannot seem to get the CTAN noweb package correctly installed for my
| Latex installation. I guess I am somewhat spoiled by the Synaptic
| package manager. Here is the result of my best attempt to get the
| noweb package installed:
i) No external noweb package is needed
ii) Synaptic is not used to install CRAN / CTAN packages
iii) Everything should be provided by r-base-core and tetex-extra.
Since relatively recently, a 'Sweave' command has been added. So simply do
$ R CMD Sweave example-1.Snw
$ pdflatex example-1.tex
$ kpdf example-1.pdf# or xpdf, or gv, or ...
| A bunch of errors. What am I doing wrong? Any help is much
| appreciated!
You simply make your life too complicated when Debian and Ubuntu make it
easier for you :)
| Of course, if there is a better place for me to ask this question
| please let me know where! Thanks!
The r-sig-debian list is appropriate for problems with Debian / Ubuntu.
Dirk
PS I usually use simple shell wrappers like this one. Others prefer
Makefile.
[EMAIL PROTECTED]:~ cat /home/edd/bin/sweave
#!/bin/bash -e
function errorexit () {
echo Error: $1
exit 1
}
function filetest () {
if [ ! -f $1 ]; then
errorexit File $1 not found
fi
return 0
}
if [ $# -lt 1 ]; then
errorexit Need to specify argument file
fi
BASENAME=$(basename $1 .Rnw)
RNWFILE=$BASENAME.Rnw
filetest $RNWFILE
echo library(tools); Sweave(\$RNWFILE\) \
| R --no-save --no-restore --slave
LATEXFILE=$BASENAME.tex
filetest $LATEXFILE pdflatex $LATEXFILE
PDFFILE=$BASENAME.pdf
#filetest $PDFFILE acroread $PDFFILE
#filetest $PDFFILE xpdf $PDFFILE
filetest $PDFFILE kpdf $PDFFILE
--
Hell, there are no rules here - we're trying to accomplish something.
-- Thomas A. Edison
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Help: Upgrading to R2.5 on Ubuntu (Feisty)
Thank you in advance for reading this help request. I am pretty new to R. I am experiencing some issues getting 2.5 installed on my Ubuntu Fiesty system and seek your advice. To the best of my ability I followed the instructions here: http://cran.r-project.org/bin/linux/ubuntu/README Setting this as the last line in my sources.list: deb http://cran.fhcrc.org/bin/linux/ubuntu feisty/ When I typed in: [EMAIL PROTECTED]:/usr/local/lib/R/site-library$ sudo apt-get install r-base Reading package lists... Done Building dependency tree Reading state information... Done r-base is already the newest version. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. [EMAIL PROTECTED]:/usr/local/lib/R/site-library$ But when I go to R and check my version: version _ platform i486-pc-linux-gnu arch i486 os linux-gnu system i486, linux-gnu status major 2 minor 4.1 year 2006 month 12 day18 svn rev40228 language R version.string R version 2.4.1 (2006-12-18) My version is still 2.4.1. I must be missing something. What do I need to do to get R version 2.5 installed on my ubuntu feisty (7.04) system? Let me know if there is any additional information I need to give to be helped out with this. Thank you for taking a look at this, Sincerely, Matt __ 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.
[R] Fwd: Help: Upgrading to R2.5 on Ubuntu (Feisty)
This fixed my problem: Thanks! Did you run 'sudo apt-get update' as well so that it actually reads the listing at CRAN / FHCRC ? What does 'apt-cache policy r-base' show? [ It should display the different vertsions it knows about; if you only see 2.4.1 then you have a problem which may just be the missing 'apt-get update' ] Hth, Dirk -- Forwarded message -- From: M. Jankowski Date: Jun 18, 2007 3:34 PM Subject: Help: Upgrading to R2.5 on Ubuntu (Feisty) To: r-help@stat.math.ethz.ch Thank you in advance for reading this help request. I am pretty new to R. I am experiencing some issues getting 2.5 installed on my Ubuntu Fiesty system and seek your advice. To the best of my ability I followed the instructions here: http://cran.r-project.org/bin/linux/ubuntu/README Setting this as the last line in my sources.list: deb http://cran.fhcrc.org/bin/linux/ubuntu feisty/ When I typed in: [EMAIL PROTECTED]:/usr/local/lib/R/site-library$ sudo apt-get install r-base Reading package lists... Done Building dependency tree Reading state information... Done r-base is already the newest version. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. [EMAIL PROTECTED]:/usr/local/lib/R/site-library$ But when I go to R and check my version: version _ platform i486-pc-linux-gnu arch i486 os linux-gnu system i486, linux-gnu status major 2 minor 4.1 year 2006 month 12 day18 svn rev40228 language R version.string R version 2.4.1 (2006-12-18) My version is still 2.4.1. I must be missing something. What do I need to do to get R version 2.5 installed on my ubuntu feisty (7.04) system? Let me know if there is any additional information I need to give to be helped out with this. Thank you for taking a look at this, Sincerely, Matt __ 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.
[R] Need Help with robustbase package: fitnorm2 and plotnorm2
This is my first post requesting help to this mailing list. I am new
to R. My apologies for any breach in posting etiquette. I am new to
this language and just learning my way around. I am attempting to run
some sample code and and am confused by the error message:
Loading required package: rrcov
Error in fitNorm2(fdat[, FSC-H], fdat[, SSC-H], scalefac = ScaleFactor) :
Required package rrcov could not be found.
In addition: Warning message:
there is no package called 'rrcov' in: library(package, lib.loc =
lib.loc, character.only = TRUE, logical = TRUE,
that I get when I attempt to run the following sample snippet of code.
The error above is taken from the code below. I am running Ubuntu
Linux with all the r packages listed in the Synaptic package manager
(universa). I loaded the prada bioconductor package as instructed in
the comments and the robustbase was downloaded and installed with the
command: sudo R CMD INSTALL robustbase_0.2- 7.tar.gz, the robustbase
folder is in /usr/local/lib/R/site-library/ When I type in
'library(robustbase)' no error appears; I believe robustbase is
installed correctly. The sample code was taken from FCS-prada.pdf. The
sample code was written in 2005, I understand that rrcov was made part
of the robustbase package sometime in the past year. This may be the
cause of the problem, but, if it is, I have no idea how to fix it.
Thank you in advance for helping out!
Below you will find the code that generates the error and the complete
output of the code. Let me know what I can do to get up and running!
Matt
#prada Bioconductor package
#http://www.bioconductor.org/repository/devel/vignette/norm2.pdf
# To install prada
#source(http://www.bioconductor.org/biocLite.R;)
#biocLite(prada)
library(prada)
filepath - system.file(extdata, fas-Bcl2-plate323-04-04.A01, package = pra
da)
print(filepath)
sampdat - readFCS(filepath)
fdat - exprs(sampdat)
print(dim(fdat))
print(colnames(fdat))
plot(fdat[, FSC-H], fdat[, SSC-H], pch = 20, col = #303030, xlab = FSC,
ylab = SSC, main = Scatter plot FSC vs SSC)
#All of this goes as the help documentation suggests it should
# 2. Show selections for various scale factors
savepar - par(mfrow=c(2,2))
for (Scalefactor in c(1.0, 1.5, 2.0, 2.5) )
{
# The next line gives the error I've included below.
nfit - fitNorm2 (fdat[, FSC-H], fdat[, SSC-H], scalefac = ScaleFactor)
plotnorm2(nfit, selection = TRUE, ellipse = TRUE,
xlab=FSC-H, ylab=SSC-H,
main=paste(SSC-H vs. FSC-H (ScaleFactor=,ScaleFactor,), sep=
))
}
par(savepar)
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()' or start with 'help(Biobase)'. For details
on reading vignettes, see the openVignette help page.
Loading required package: RColorBrewer
Loading required package: grid
Loading required package: geneplotter
Loading required package: annotate
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
[1] /usr/local/lib/R/site-library/prada/extdata/fas-Bcl2-plate323-04-04.A01
[1] 21158
$P1N$P2N$P3N$P4N$P5N$P6N$P7N$P8N
FSC-H SSC-H FL1-H FL2-H FL3-H FL2-A FL4-H Time
Loading required package: rrcov
Error in fitNorm2(fdat[, FSC-H], fdat[, SSC-H], scalefac = ScaleFactor) :
Required package rrcov could not be found.
In addition: Warning message:
there is no package called 'rrcov' in: library(package, lib.loc =
lib.loc, character.only = TRUE, logical = TRUE,
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
