Displaying 20 results from an estimated 1000 matches similar to: "Re: Need help on how to list functions from a loaded package..."
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-----
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.
2004 Jan 20
2
graph algorithms in R
Hi,
I was wondering if there are any packages available that can represent
mathematical graphs along with functions to manipulate them? Google
did'nt turn up anything ( I may be asking too much of R :-/ )
Thanks,
-------------------------------------------------------------------
Rajarshi Guha <rxg218 at psu.edu> <http://jijo.cjb.net>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04
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)
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
2002 Mar 06
3
Problem in .First.lib
Hello!
I downloaded a package "multtest" (from bioconductor.org) in R, and
installed it by 'R CMD <package>' (after unzipping and taring).
The problem is when I say 'library(multtest)' in R, the following error is
generated:
Error in dyn.load(x, as.logical(local), as.logical(now)) :
unable to load shared library
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 13
6
permutation-based FDR
Hola a todos,
Tengo un pequeño problemilla...
Tengo unas 9000 variables que he contrastado con 1 en concreto con el test
de wilcoxon. He calculado el p-valor, y queria corregirlo con el
permutation-based FDR. He encontrado una funcion con R comp.fdr()que hace
esta corrección, pero te pide que le pongas las variables con las
observaciones y te hace el test (según he entendido). Yo solo quiero
2010 Mar 03
1
Help with multtest (rawp2adjp)
Hello R experts,
I am trying to analyze this dataset and am stuck on this problem for quite
some time now.
I am using mt.rawp2adjp.
the output that came out was a matrix with two colums since I had asked it
to calculate the adjusted p values using one method.
so it has the two columns as: rawp BH
I combined these using cbind with my actual dataframe.
checked using head all was fine.
thereafter I
2006 Aug 31
1
problem with postscript output of R-devel on Windows
I have developed a problem with the postscript output of plot on Windows. My code still works properly with R 2.3 but, with R 2.4, the white text on red background does not show up. It does, however, show up when output is sent to the screen. Below is my code and sessionInfo.
R version 2.4.0 Under development (unstable) (2006-08-29 r39012)
i386-pc-mingw32
locale:
LC_COLLATE=English_United
2017 Oct 10
2
small files performance
2017-10-10 8:25 GMT+02:00 Karan Sandha <ksandha at redhat.com>:
> Hi Gandalf,
>
> We have multiple tuning to do for small-files which decrease the time for
> negative lookups , meta-data caching, parallel readdir. Bumping the server
> and client event threads will help you out in increasing the small file
> performance.
>
> gluster v set <vol-name> group
2017 Oct 10
0
small files performance
I just tried setting:
performance.parallel-readdir on
features.cache-invalidation on
features.cache-invalidation-timeout 600
performance.stat-prefetch
performance.cache-invalidation
performance.md-cache-timeout 600
network.inode-lru-limit 50000
performance.cache-invalidation on
and clients could not see their files with ls when accessing via a fuse
mount. The files and directories were there,
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 =
2007 Nov 02
0
loading installes package including all needed subpackages
Hallo,
I just installed all needed packages for my project on my PC. But I cannot load all at one time. I now want to load limma. How can I realize the following plan: I want to install for example limma inclusive all needed other sub packages (add-on). Can anyone tell me the corresponding command?
Thanks, Corinna
Here is the result of the command library():
Pakete in Library
2008 Jan 14
1
stochastic growth rate (package biopop)
Dear all,
I am running matrix population models using package "popbio".
In a deterministic model {i.e., transition matrix is defined as A <-
matrix(c(0.70, 0.70,0.35,0.50), nrow=2,byrow=TRUE}, population growth rate
can be estimated from the dominant eigenvalue {command "eigen.analysis"}.
However, I cannot figure out the way to compute the asymptotic stochastic
population
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
2012 Nov 14
0
Generating autogressive model in R
Dear R users,
Please help me with the following problem. I have a data set of the form ´dat´
dat <- data.frame(id = seq(1:5), trt=c(0,0,1,1,1),tid=c(0,0,0,0,0),
ntid=c(0,0,0,0,0))
The function auto is used to generate the autoregressive model:
auto <- function(seed,delta,beta,maxt,dat){
set.seed(seed)
sp <- lapply(split(dat,dat$id),function(x){
while(x$tid <