Displaying 20 results from an estimated 400 matches similar to: "Error: cannot allocate vector of size..."
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 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
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2007 Sep 24
2
how to export.RDA file to a text file?
Hi,
Does anyone know how to export .RDA file (in R program) to a normal text file
(readable by any text editor)? Also, how to export an object in R program into a
text file (not .RDA file)?
Thank you.
Jittima
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 =
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",
2007 Sep 24
2
What is RDA file and how to open it in R program?
Hi,
I have a set of gene expression data in .RDA file. I have downloaded
Bioconductor and R program for analyzing these data. Anyway, I am not sure how
to open this RDA file in R program (what is the command?) in order to look at
these data. And which package should I use for analyzing it e.g. plot the
expression image?
Thank you.
Jittima
2006 Oct 11
1
Possible bug in accessing methods documentation?
Hi,
Reading help("Documentation"), I'm led to believe that a help call
like:
?myFun(x, sqrt(wt))
Will search for help on the appropriate method in the case that myFun
is generic. This isn't working for me. Here is an example using the
Biobase package:
## If Biobase is not installed
source("http://bioconductor.org/biocLite.R")
biocLite("Biobase")
2007 Dec 20
1
custom subset method / handling columns selection as logic in '...' parameter
Dear R-helpers & bioconductor
Sorry for cross-posting, this concerns R-programming stuff applied on
Bioconductor context.
Also sorry for this long message, I try to be complete in my request.
I am trying to write a subset method for a specific class (ExpressionSet
from Bioconductor) allowing selection more flexible than "[" method .
The schema I am thinking for is the following:
2006 Oct 11
1
Possible bug in accessing methods documentation? (PR#9291)
On 10/11/2006 2:48 PM, Seth Falcon wrote:
> Hi,
>
> Reading help("Documentation"), I'm led to believe that a help call
> like:
>
> ?myFun(x, sqrt(wt))
>
> Will search for help on the appropriate method in the case that myFun
> is generic. This isn't working for me. Here is an example using the
> Biobase package:
>
> ## If Biobase is
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 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
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
2011 Oct 07
1
Creating One Single Object with Phenotype and Expression Data
Hey,
I have code that can check the quality of a data set we're working with
(expression data), and I'm having some trouble writing code that would make
the expression data we have tie to other data we want to link it to (called
phenotype data). Does anyone have any advice on how I could make a single
object that would do this? Other relevant info: I want to use the pdata()
function,
2010 May 27
2
Methods to explore R data structures
Hi,
I'm very confused about R structures and the methods to go with them. I'm
using R for microarray analysis with Bioconductors. Suppose without reading
the documentations, what's the best way to explore a data structure when you
know nothing about it?
I am currently using is() / class() to see what the object is. str() /
attributes() to probe inside the object, and
2013 May 08
1
Namespace/inheritance problem in S4 methods for a union class
Hi,
I started this post on bioc-devel but this seems to be more general:
https://stat.ethz.ch/pipermail/bioc-devel/2013-May/004311.html
See reproducible example from Martin below.
Thank you.
Renaud
---------- Forwarded message ----------
From: Martin Morgan <mtmorgan at fhcrc.org>
Date: 7 May 2013 19:55
Subject: Re: [Bioc-devel] ExpressionSet and LumiBatch: inheritance problem
in S4
2011 Nov 20
1
Deleting multiple rows from a data matrix based on exp value
Dear List,
I have a data matrix that consists of ~4500 rows and 25 columns (i.e.
an exprSet object that I converted via the 'exprs' function into a
data matrix)
Now I want to remove/delete the rows where all exp. values in that
particular row are below or equal to a specific cut-off value (e.g
1.11)
I have tried using several commands to address this issue:
>Matrix[rowSums(Matrix
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
2009 Oct 22
1
S4 object??
Hi all,
I have loaded the LIMMA and Biobase package and tried these commands:
library(limma)
library("Biobase")
data <- read.table("c:/temp/data.txt",header=T,row.names=1)
ExpressionData <- as.matrix(data[,c(2,3,4,6,7,8)])
eset <- new("ExpressionSet", exprs = ExpressionData)
design <- cbind(WT=1,P=c(0,1,1,0,1,1),G=c(0,1,0,0,1,0))
fit <-
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:
>
2007 Nov 28
1
Can't make affylmGUI work
Hi,
Can anyone help me of the affylmGUI package, I can't get it work and
searched for google but can't find any proper solutions.
I get the error information each time when I load my cells files, which
are shown in the following links.
-------------
http://clarezoe.googlepages.com/1.png
http://clarezoe.googlepages.com/2.png
http://clarezoe.googlepages.com/3.png
-------------
Errors also