Displaying 20 results from an estimated 300 matches similar to: "S4 Method Collisions with "[" (PR#4075)"
2003 Sep 02
1
completeSubclasses() methods bug (PR#4051)
Full_Name: Colin A. Smith
Version: 1.8.0
OS: Mac OS X 10.2.6
Submission from: (NULL) (128.102.184.81)
annaffy 1.0.1 (in BioC CVS) fails to load. annaffy 1.0 (on the BioC web site)
has the same problem.
It looks like the load is failing because of a bug in completeSubclasses() in
r-devel. It calls setIs() and doesn't specify an environment via the "where"
argument. setIs()
2008 Mar 20
2
Error in function (classes, fdef, mtable): unable to find an inherited method for function "indexProbes", for signature "exprSet", "character"
Hello Everyone,
I am writing programs in R from 7 months and I am able to solve most of the
errors/issues except for this current post.
My Task is to read a Microsoft Excel file(textE_to_affy.csv) which contains
the Microarray Expression Values collected from the Illumina Microarray
experiment. These collected intensity values need to be normalized(Rank
Invariant Normalization) by using the R
2008 Feb 27
2
problem with creation of eSet
Hi,
I am having troubles with creating an eSet and would appreciate any help on
the following problem.
I am trying to create an eSet using the following code
pd <- read.table(file="pdata.txt",header =TRUE,row.names=1);
colnames(pd) <- c("type","tumor","time","id");
pdN <- list(type =
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 =
2008 Jan 03
1
help with combining matrix and list into dataframe
Problem#################################################################
I am having a problem combining a matrix and elements of a list into one data
frame.
Data####################################################################
The matrix is ludwig.results and dim of matrix is 213,8.
The list is called symbols and its length is 213.
Following is an example the structure of my matrix
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
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
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
2006 Feb 20
1
mva.pairs
Hello,
I am using the following code to plot an MVA plot.
library(affy)
library(Biobase)
library(limma)
library(gcrma)
pd<-read.phenoData("Clk.targets.2.txt",header=TRUE,
row.names=1,as.is=TRUE,sep="\t")
Data <- ReadAffy(filenames=pData(pd)$FileName,phenoData=pd)
Print(Data)
eset <- gcrma(Data)
write.exprs(eset,
2006 Jul 25
1
Drosophila Genome 2.0 annaffy annotation
Dear all,
I am currently analyzing a set of arrays hybe on the lattest affy Drosophila
2.0 GeneChip. I am trying to run simple annaffy analysis but canĀ¹t find what
is the name of the annotation file I need to use.
Here is the output of the AffyBatch object I am using:
> expData
AffyBatch object
size of arrays=732x732 features (16749 kb)
cdf=Drosophila_2 (18952 affyids)
number of samples=4
2008 Dec 15
3
install.packages and dependency version checking
I've started to implement checks for package versions on dependencies in
install.packages(). However, this is revealing a number of
problems/misconceptions.
(A) We do not check versions when loading namespaces, ahd the namespace
registry does not contain version information. So that for example
(rtracklayer)
Depends: R (>= 2.7.0), Biobase, methods, RCurl
Imports: XML (>=
2003 Oct 30
0
Release of Bioconductor 1.3
The Bioconductor core group would like to announce the 1.3 release of
the Bioconductor software. There are many new packages as well as
several major upgrades and fixes in older packages, and users are
encouraged to check them out. Release 1.3 is intended to be operated
with R version 1.8.X, which can be obtained at CRAN
(http://cran.r-project.org/)
-- WHAT FEATURES DOES THIS RELEASE PROVIDE?
2003 Oct 30
0
Release of Bioconductor 1.3
The Bioconductor core group would like to announce the 1.3 release of
the Bioconductor software. There are many new packages as well as
several major upgrades and fixes in older packages, and users are
encouraged to check them out. Release 1.3 is intended to be operated
with R version 1.8.X, which can be obtained at CRAN
(http://cran.r-project.org/)
-- WHAT FEATURES DOES THIS RELEASE PROVIDE?
2008 Mar 08
3
expression matrix
Hello,
I am to run this R script but i keep getting this error.
> expr<-exprs(golubMerge)
Warning message:
The exprSet class is deprecated, use ExpressionSet instead
I tried to find information on the website but no luck. (exprSet...etc)
thank you.
--
View this message in context: http://www.nabble.com/expression-matrix-tp15912874p15912874.html
Sent from the R help mailing list archive
2007 Sep 24
1
Error: cannot allocate vector of size...
Hi,
I want to change .RDA file to a text file. So I did as follows.
>load("my.rda")
>ls() ---> then it showed [1] exprs
>write.table(exprs,"C:\\my.txt",sep="\t")
I was successful with the first .RDA file. Then I used the same commands with
another .RDA file (172 MB)which is 4 times bigger than the first file (41.2 MB).
When I put the last command
2003 Oct 27
1
initialization of S4 classes/methods
I'm seeing weird issues in methods initialization, i.e. loading
marrayClasses loads Biobase, and when explicitly done, as in
library(Biobase)
library(marrayClasses)
is fine, but when Biobase is loaded via a require statement in
marrayClasses' .First.Lib, I end up with:
Warning message: In the method signature for function "coerce", class
"exprSet" has no
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 May 30
1
A question about *read.table()*
Hi list,
I have a question about using *read.table()* to read in a txt file.
Basically, it
consists of 16346 rows, 6 columns (no header). The code I used is:
exprSet <- read.table('process_all4_GSA2.txt', row.names = 1,header =FALSE)
and I got an error message:
> exprSet <- read.table('process_all4_GSA2.txt', row.names = 1,header
=FALSE)
Error in
2003 Dec 26
1
Problems converting output from Sweave to PDf
I am having trouble converting the output from Sweave
into a valid PDF file.
I have created a simple .Rnw file which will become a
full vignette at some point, but during the
intermediate testing, I got errors from texi2dvi.
This is what I have done.
0) Using a Windows Xp system
1) Created a file called GeneSpring.Rnw
2) Convert this to Tex using Sweave("GeneSpring.Rnw")
from within R