Displaying 20 results from an estimated 7000 matches similar to: "Problem in .First.lib"
2003 Sep 11
1
S+DOX eqivalent in R?
Dear List,
I am looking for a function `Pseudo standard error' (PSE), which is
available in S+ DOX (design of experiemnt) module - Is there a similar
function available in R?
Reference for PSE function is in the paper:
'Quick and easy analysis of unreplicated factorials' by Russell V. Lenth,
Technometrics, 1989, 31, 4, 469-473.
Thanks.
-Nitin
2007 May 30
3
separate y-limits in xYplot panels
Hello,
I would like to get the scales of y-axes dependent only on the data points in a particular panel. Have attached a test example below.
When using 'relation="free"', it does not make the scales 'free', however when using 'relation="sliced"', I get a warning "Explicitly specified limits ignored in: limitsFromLimitlist(have.lim = have.ylim, lim
2005 Dec 20
2
Extracting data from .zip file in WINDOWS version of package
Hello,
I am building a R-package for Genetics analysis. The accepted data is in pedigree (.ped) file format.
To load the data (say CAMP.ped) from "data" directory, I have a function "CAMP.R", which does the job.
The package builds successfully in Linux (.tar.gz) and the data loads successfully by "data(CAMP)".
However, when I build the package in WINDOWS, the data
2005 Oct 20
2
Error in building package indices
Dear R-devel members,
We are building a new package (GeneticsBase) for analysis of genetic data .
While doing "R CMD check with R-2.1.1, I am getting the following error:
** building package indices ...
Error in "colnames<-"(`*tmp*`, value = c("family", "pid", "father",
"mother", :
length of 'dimnames' [2] not equal to
2004 Jan 20
1
Re: Need help on how to list functions from a loaded package...
To All
How does one get a list of functions from a loaded package so that one can
then get the appropriate help for each of the functions. Currently my
method is
based on a lot of trial-and-error.
Here's an example of what I mean...
>From this forum I learn that an interesting package called "multtest" exists
on Bioconductor.
I then use R Console's "Packages" --
2006 Jun 29
2
Biobass, SAGx, and Jonckheere-Terpstra test
Hi list,
I tried to load the package SAGx and failed because it complains it's
looking for the Biobass which is not there. Then I looked up the package
list and Biobass is not found.
I'm trying to run the Jonckheere-Terpstra test and from what I see in
the R archive, SAGx is the only place it's been implemented.
> library(SAGx)
Loading required package: multtest
Loading required
2006 Feb 01
1
R CMD check barfs at 'suggested' package
I have been running R CMD check for the first time on of our own
packages, which otherwise builds, installs and runs just fine. The
package depends on package akima and suggests package multtest;
suggesting multtest is indicated because a) it loads a lot of other
Bioconductor packages, very slowly, and b) it is only needed for one
specific subroutine, which executes require(multtest)
2005 Oct 10
1
bug loading libraries with winXP and 2.2.0 but not 2.1.1 (PR#8200)
Full_Name: Ken Kompass
Version: 2.2.0
OS: winXP pro (2002 version, SP2)
Submission from: (NULL) (128.252.149.244)
Using R2.2.0 I get this error msg when loading certain bioconductor libraries
(depending on whether the library contains file named "all.rda" in R folder of
library) :
> library(multtest)
Error in open.connection(con, "rb") : unable to open connection
In
2010 Nov 12
1
installing dependencies: binary vs source
Hi,
Installing from binaries on Windows:
> install.packages("multtest")
Warning: dependency 'Biobase' is not available
trying URL
'http://cran.fhcrc.org/bin/windows/contrib/2.12/multtest_2.6.0.zip'
Content type 'application/zip' length 1645590 bytes (1.6 Mb)
opened URL
downloaded 1.6 Mb
package 'multtest' successfully unpacked
2006 Feb 01
1
Rd files with unknown sections
Hi,
With recent versions of R-devel, "R CMD check" complains about
some "Rd files with unknown sections".
hpages at gladstone:~> R CMD check multtest_1.9.4.tar.gz
...
...
* checking Rd files ... WARNING
Rd files with unknown sections:
/home/hpages/multtest.Rcheck/00_pkg_src/multtest/man/boot.resample.Rd:
notes
2011 Nov 30
1
install "multtest" and "preprocessCore" packages in Bioconductor library
Hi Nguyen,
> Subject: [R] install "multtest" and "preprocessCore" packages in
> Bioconductor library
> Date: Wed, 30 Nov 2011 09:57:36 -0800
> From: UyenThao Nguyen <unguyen at tethysbio.com>
> To: r-help <r-help at r-project.org>
> CC: uth.nguyen at ucdavis.edu <uth.nguyen at ucdavis.edu>
>
> Hi All,
>
> I've tried to
2010 Jul 18
5
package "plotrix"
I installed package plotrix because reading its vignette it looks like it can help me solve a "legend" problem.
The package instaleed correctly on my Mac OS/X 10.5.8
But I cannot reproduce the examples centered on function "lgendg".
> library(plotrix)
> plot(0.5,0.5,xlim=c(0,1),ylim=c(0,1),type="n",
+ main="Test of grouped legend function")
>
2005 Dec 18
1
package unlisted (PR#8410)
Full_Name: Cesar Henrique Torres
Version: 2.2.0
OS: winXP-pro
Submission from: (NULL) (201.1.196.50)
Hi developer's!
I'd like to know were gtools package is, because in the link below it isn't:
http://cran.r-project.org/bin/windows/contrib/r-release/
This package is used in gplots and I'm trying to make a balloonplot.
Thanks a lot,
Cesar Torres.
2006 Nov 18
1
Why SAM has totally diffent results in R2.1.1 and R2.4.0
Hi,
I am using SAM (from siggenes_1.2.11 package) method to select genes from
a microarray data set. After installing the latest R2.4.0 on my computer, to
my surprise the results are totally different from that calculated using
R2.1.1. Even the example code doesn't work the same way under these two
versions of R. Does anybody know what is going on? Thanks for any
suggestions.
2003 Sep 04
2
problem with samba 3.0 beta
Hi!
I am using samba 3.0 beta as a PDC with ldap authentication.
I am able to login to win 98 machine with samba as PDC.
The problem i am facing is samba requires /etc/passwd entry of user in addition
to ldap entry. I am pasting my smb.conf for ref.
Is it possible to use only ldap account so that i do not have to add /etc/passwd
entry.
I have not added ldap entry in /etc/nsswitch.conf file.
2010 Jul 08
2
package installation for Windows 7
Neither biocLite nor the GUI menus can install packages on my system.
Here is relevant output:
> version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 11.1
year 2010
month 05
day 31
svn rev 52157
language R
version.string R version 2.11.1 (2010-05-31)
> source("http://bioconductor.org/biocLite.R")
BioC_mirror =
2006 Dec 20
1
SFTP
Where do I need to specify the password in SFTP program to run it in an non-interactive mode.
2007 Jan 23
3
the value of Delta
Dear all,
I am running R 2.4.1.
> library(siggenes);
> library(multtest);
> cl<-rep(c(0,1),c(3,3));
> sub<-exprs(AffyExpData[,c(1:3,7:9)]);
> gn<-geneNames(AffyRAwData);
> sam.out<-sam(sub,cl,rand=123,gene.names=gn);
We're doing 20 complete permutations
> sam.out
SAM Analysis for the Two-Class Unpaired Case Assuming Unequal Variances
Delta p0
2004 Jan 20
0
Re: Need help on how to list functions from a loaded pack age...
You can get help on the whole package by
> help(package="multtest")
which is likely pretty close to what you want. There's the index etc for the
package on the web as well. You can also just look in the package's
installation directory. If it's loaded you can do an ls(2) say if it loaded
in position 2, to get all objects in the package.
Reid
-----Original Message-----
2008 Mar 01
2
Newbie: Incorrect number of dimensions
> dim(data.sub)
[1] 10000 140
#####extracting all differentially express genes##########
library(multtest)
two_side<- (1-pt(abs(data.sub),50))*2
diff<- mt.rawp2adjp(two_side)
all_differ<-diff[[1]][37211:10000,]
all_differ
#####list of differentially expressed genes##########
> probe.names<-
+ all_differ[[2]][all_differ[[1]][,"BY"]<=0.01]
Error in