Displaying 20 results from an estimated 3000 matches similar to: "Release of Bioconductor 1.3"
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
2003 May 29
0
Bioconductor 1.2 Released
The Bioconductor development team announces release 1.2 of the
Bioconductor packages for the analysis of genomic data. Bioconductor
is an open source bioinformatics software project based on the R language.
Version 1.2 features:
=====================
* All packages from the 1.1 release are included. All current bug
fixes have been applied, and most have been upgraded and
provide enhanced
2006 Aug 11
1
[BioC] problem loading affycoretools (more details)
Hi again,
I have been playing around with the order of loading packages, and as far
as I can tell, there's nothing specific with affycoretools that's causing
my Rgui to crash (i.e., shuts down and the Microsoft 'please send error
report' box pops up). Instead, it has something to do with the order & type
of packages that are loaded that add items to the menu bar by
2008 Jun 19
1
Installation Error with Bioconductor on R
Hi, I am trying to install Bioconductor onto R version 2.7.0 for Windows. I installed R, then followed the instructions on http://www.bioconductor.org/download, which state that you should type the following:
source("http://bioconductor.org/biocLite.R")
biocLite()
When I do that, I get the following error:
Running biocinstall version 2.2.9 with R version 2.7.0
Your version of R
2010 Jan 29
1
combine 3 affybatches
Hello,
Im trying to combine 3 affybatches (1x hgu133+2 array and 2x hgu133a array)
Im useing this script:
library(matchprobes)
library(affy)
library(AnnotationDbi)
library(hgu133plus2probe)
library(hgu133aprobe)
library(hgu133a.db)
u133p2 = ReadAffy() # reading hgu133 +2 cel file into affybatch
u133a1 = ReadAffy() # reading hgu133a cel file into affybatch
u133a2 = ReadAffy() # reading hgu133a
2005 Aug 31
1
Bioconductor and R-devel
Hi,
I have built R (current development version) and BioConductor 1.7
with portland group compiler on a AMD Opteron.
When I ran qc assessment on Affymetrix latin square data set, I got the
following output,
Loading required package: affy
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view,
2003 Aug 07
5
gregmisc
Hi
How do I install "gregmisc" packages?
I did-
% sudo R
> install.packages("gregmisc")
.
.
> barplot2()
but,
Error: couldn't find function "barplot2"
--
atuya
Mac OSX 10.2.6
R 1.7.1
2007 Mar 23
1
can't load just saved R object "ReadItem: unknown type 65"
I have run into a problem loading a just saved R object using R-devel. I
have been saving and loading this particular type of R object for a long
while and never ran into this problem. I save, then immediately reload
(to test save) and get "ReadItem: unnknown type 65".
This error is reproducible after logout from server and restart of emacs
and R.
Below is my output and
2007 Mar 23
1
can't load just saved R object "ReadItem: unknown type 65"
I have run into a problem loading a just saved R object using R-devel. I
have been saving and loading this particular type of R object for a long
while and never ran into this problem. I save, then immediately reload
(to test save) and get "ReadItem: unnknown type 65".
This error is reproducible after logout from server and restart of emacs
and R.
Below is my output and
2003 Mar 26
1
formal methods and classes and capitalization conventions
Martin Maechler has suggested that I post this comment to r-devel. It was
originally posted to bioconductor.
---------------------------------
I'd like to raise the issue of a capitalization convention for naming
objects in R. Almost everything in R used to be lowercase but recently
there is increasing use of mixed upper/lower case to define names. There is
potential for using the
2005 Oct 18
2
Installing Bioconductor on R
hi all,
Am new to R. I am having problems installing Bioconductor package in
R on fedora core 4 running on AMD64 bit machine.
this is the error message I get :
gcc -shared -L/usr/local/lib -o affyPLM.so avg_log.o biweight.o
chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o
idealmismatch.o LESN.o lm.o lm_threestep.o log_avg.o matrix_functions.o
2007 Mar 23
0
can't load just saved R object using R-devel "ReadItem: unknown type 65"
I am unable to load a just saved R object. Get message "ReadItem:
unknown type 65" I am using R-devel and the problem is reproducible
after logout and restarting R.
Output and sessionInfo() below.
Mark
> setwd("~/Genomics/Experiments.Genomic/BB01/acb.shell")
> local(save(affy.object.preprocessed, file
="affy.object.preprocessed.R" ))
>
2004 May 17
0
Bioconductor 1.4 released
Greetings!
The Bioconductor core group would like to announce the 5th release of
Bioconductor, version 1.4. There are many new packages as well as
several major upgrades and fixes in older packages, and users are
encouraged to upgrade existing tools and check out the new packages.
Release 1.4 is intended to be operated with R version 1.9.x, which can
be obtained at CRAN
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 Apr 28
1
normalizing affy data caused an error
Hi all,
I tried to do normalization of affymetrix data with bioconductor on a
Linux server. When I read in the cel files all seemed ok. But the next
step caused an error. With Win XP all works fine. Did anyone experience
similar problems?
Thanks,
Thomas
> PI <- ReadAffy()
> PI
AffyBatch object
size of arrays=712x712 features (14 kb)
cdf=ATH1-121501 (??? affyids)
number of
2007 Feb 28
1
problem with help.start and ?somefunction
Hi all,
I am going to be teaching a workshop next week using R and Bioconductor in one of our university's computer labs. They have recently installed R 2.4.1 for me, and I'm checking all my scripts. I just noticed that using the ?somefunction call to access the documentation for that function is not working. On my own PC, the ? call output changed between R 2.3 and 2.4; before it would
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
2006 Nov 11
1
Install bioconductor
Hello useRs,
I'm trying to install bioconductor on ubuntu edgy eft and R 2.4.0.
I have some error messages during installation, in particular for the
package "affy" :
"Error: package 'affy' required by 'makecdfenv' could not be found"
I have tryed to install 'makecdfenv' with the command :
getBioC("makecdfenv")
But I have this message
2006 Oct 12
1
getMethods() not finding all methods
Running R2.4.0 on Apple Mac OS X 10.4.8,
in Emacs ESS mode, and also R.app.
In an attempt to learn a bit more about
a particular method (geneNames in package affy)
I invoked
getMethods("geneNames")
which produced geneNames methods, but not the
one in affy (output below).
I had to know the signature (AffyBatch) in order
to find the method
> getMethod("geneNames",
2011 Feb 25
1
limma function problem
Hi,
I have two data set of normalized Affymetrix CEL files, wild type vs Control
type.(each set have further three replicates).
> wild.fish
AffyBatch object
size of arrays=712x712 features (10 kb)
cdf=Zebrafish (15617 affyids)
number of samples=3
number of genes=15617
annotation=zebrafish
notes=
> Dicer.fish
AffyBatch object
size of arrays=712x712 features (10 kb)
cdf=Zebrafish (15617