Displaying 20 results from an estimated 1000 matches similar to: "formal methods and classes and capitalization conventions"
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",
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
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?
2010 Jan 31
2
Using apply function on duplicates in a data.frame
Dear R-Helpers,
I have a data.frame (df) and the head of data.frame looks like
ProbeUID ControlType ProbeName GeneName SystematicName
1665 1577 0 pSysX_50_22_1 pSysX_50 pSysX_50
5422 5147 0 pSysX_49_8_1 pSysX_49 pSysX_49
4042 3843 0 pSysX_51_18_1 pSysX_51 pSysX_51
3646 3466 0 sll1514_0_2 sll1514 sll1514
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
2004 Sep 09
1
Confused about loading other packages from a package
In my package, I create a new method for plot with the following signature:
setMethod("plot", signature(x="marrayNorm", y="formula"), plot.ma)
where marrayNorm is a class defined in the marray package. After
building and installing my package, I get the following warnings when
I load my package (with library(maVis)):
Warning messages:
1: In the method signature
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
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
2011 Jun 28
1
help required for GO Annotation problem
Hello,
I basically want to use R-help, and post some problems which I am facing. The Ref is a well known Genome Biology paper "Bioconductor: open software development for computational biology and bioinformatics" by Robert C Gentleman et al., 2004. Generating Heatmaps till Fig2 is working so I think esetSel is not the problem..
However, for generating the Figure 3, for GO annotations the
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
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 =
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
2007 Oct 25
2
Find duplicates and save their max value
Hi,
maybe someone can help me with this:
I have a matrix of genes and values:
GeneName Value
Abc1 10
Abc2 11
Bbc1 -5
Bbc31 2
Ccd 5
Ccd -2
Ccd 7
Dda 5
Dda 10
..... .....
Zzz3 -1
I would like to
2004 Jan 22
1
Calculation of normalised red and green intensities
Dear Sir/Madam,
I could succesfully normalise my microarray data using marrayNorm package.
However, i have not been able to get normalised red and green channel
intensities through R package. Is there a possibility to write a formula
to calculate back the red and green channel intensities after normalisation
of the data. Do I need to incorporate this formula in my R script? I am
biologist
2007 Apr 13
2
R on Solaris 10 x64
Hi R Developers,
Greg is helping me with debugging R on Solaris 10 x64. Please let us
know if you have any thoughts or tips that can help us debug this.
Thanks,
David
************
Using default transfer plist
in vector_io: permuting
About to write
*** caught segfault ***
address e8554000, cause 'memory not mapped'
Traceback:
1: .External("do_hdf5save", call,
2003 Sep 05
2
S4 Method Collisions with "[" (PR#4075)
Full_Name: Colin A. Smith
Version: 1.8.0
OS: Mac OS X 10.2.6
Submission from: (NULL) (216.102.90.18)
Both Biobase and my package annaffy use S4 classes to define methods for "[".
Both packages use the save image method of installation. (See annaffy 1.0.3 in
BioC CVS.)
Depending on how both packages are loaded, the Biobase definitions seem to be
getting masked out:
>
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
2003 Feb 19
3
Rcmd check does not recognize formal generic function as code object
Dear all,
I am trying to write a package using formal methods and classes from the
methods package. I have not been able to get the package to pass rcmd check
without warnings, because rcmd check does not recognize my generic
functions as code objects and therefore queries why they have documentation
entries.
I have isolated the problem in a very small trivial example which I give
below. I
2004 Dec 29
1
about image(graphics) function
Hi all,
is it possible to modify the way a graph obtained
through image(graphics) is filled, I mean starting
filling the graphical matrix by row from the
upper-left rather than by the lower-left cell... In
many cases, it can be usefull to have a representation
of the data spatialy corresponding to a real support,
as it is the case with the function image(marray) from
Bioconductor packages, which