Displaying 20 results from an estimated 110 matches similar to: "error with the function GOHyperG from GOstats package"
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
2012 Jul 21
1
GOstats: get genes for corresponding enriched GO term
Hi,
I used GOstats to perform enrichment test on a set of genes (20).
There are 7 GO terms with pvalue less than cuttoff and therefore shown in
the result table.
How can I get the information that which gene in the input gene set belong
to which GO term of these enriched GO terms?
Thanks for any comments.
best,
Tim
[[alternative HTML version deleted]]
2008 Dec 10
0
FW: Kegg.db with GOstats
-----Original Message-----
From: Robert Gentleman [mailto:rgentlem@fhcrc.org]
Sent: Wed 10/12/2008 18:47
To: Legaie, Roxane
Subject: Re: Kegg.db with GOstats
Hi Roxanne,
Can you redirect your question to the mailing list. And, you can find the
answer in the mailing list archives...
best wishes
Robert
Legaie, Roxane wrote:
> Dear Robert Gentleman,
> I am currently working on
2006 Mar 10
1
Problem using GOstats package in R 2.2.1
Dear all,
This message is a kind of 'to be continued...' for that send by /Yu-An
Dong,/ [BioC] problems with GO package data
<https://stat.ethz.ch/pipermail/bioconductor/2006-February/011760.html>,
last february.
I've just installed R 2.2.1 on my computer (Windows based version) and
downloaded Bioconductor available for this version via the graphical
interface facility
2004 Aug 18
3
calling R from Perl
Hello,
I am trying to call R from Perl running on Windows 2000. I have looked
through the previous posts regarding running R from Perl and all have
referred to the RSPerl package at Omegahat. Unfortunately the
documentation for this package specifically states that it only works in
Unix at the moment. Does anyone else have any suggestions about the best
way to do this in the Windows
2013 May 21
1
Calculating AIC for the whole model in VAR
Hello!
I am using package "VAR".
I've fitted my model:
mymodel<-VAR(mydata,myp,type="const")
I can extract the Log Liklihood for THE WHOLE MODEL:
logLik(mymodel)
How could I calculate (other than manually) the corresponding Akaike
Information Criterion (AIC)?
I tried AIC - but it does not take mymodel:
AIC(mymodel)
# numeric(0)
Thank you!
--
Dimitri Liakhovitski
2011 Sep 13
2
GO & Protein Complex Analysis for Homo sapiens
Dear All,
I need to fetch GO ontologies for Homo sapiens with their mappings to
corresponding Uniprot identifiers. I would be using this information to
compare result from a clustering algorithm with existing protein complexes.
This would be a test to check how the clustering algorithm accurately
captures GO terms with respect to the known protein complexes. Can anyone
suggest a simple workflow
2017 Jun 04
2
read.table
Hi All,
I wonder if there should be one character for quote= in read.table, i.e.,
> args(read.table)
function (file, header = FALSE, sep = "", quote = "\"'", dec = ".",
...
I have a file containing the following lines,
08248-GOTERM 3'-phosphoadenosine 5'-phosphosulfate biosynthetic process
08279-GOTERM 3'-phosphoadenosine
2017 Jun 04
0
read.table
On 04.06.2017 11:50, jing hua zhao wrote:
> Hi All,
>
>
> I wonder if there should be one character for quote= in read.table, i.e.,
>
>
>> args(read.table)
> function (file, header = FALSE, sep = "", quote = "\"'", dec = ".",
> ...
>
> I have a file containing the following lines,
>
>
> 08248-GOTERM
2007 Mar 01
1
object is not subsettable
Dear colleagues,
I've just come across a problem with the following command which is a
part of the "metaOverview.R" code file provided as an monography-
accompanying file at
http://www.bioconductor.org/docs/mogr/metadata:
##################################
R> hasChr <- eapply(GOTERM, function(x)
+ x[grep("chromosome", Term(x))])
Error in
2004 Mar 27
2
cbind question
hi, all:
Just wonder if there is any suggestions in how to get around this cbind error. I created two character lists with identical length. First tried combine the lists together with cbind, then convert the lists to matrix, and tried again. Both faied. Any fix to merge the two lists/matrices?
ll<- multiget(ftID, hgu95av2LOCUSID)
> class(ll)
[1] "list"
> sym <-
2012 Apr 03
2
how to map microarray probe to gene, homology
Hi:
I have clustered microarray gene expression data and trying to map between
microarray probe, gene, pathway, gene ontology, and homology for a set of
(affy) microarray probes. Is there any package in R which facilitates this?
I am looking at bioconductor, but till now could not find a solution. A
link to some worked example would be appreciated.
Thanks and regards.
John
[[alternative HTML
2005 Mar 29
2
Annotation metadata "kills" help.search
Greetings!
OS: Windows
R 2.0.1
Before anyone flames -- I tried to query this on the R searchable web site
and using google and did not find anything applicable.
As of about a week ago the help.search function dies when used in the simple
help.search("something") usage.
The error is
Error in rbind(...) : number of columns of matrices must match (see arg 203)
After some effort I have
2010 Mar 29
1
stuck with affy / limma
Hi,
I have a question concerning the analysis of some affymetrix chips. I
downloaded some of the data from GEO GSE11324 (see below). In doing so I'm
stuck after I identified the probesets with significant changes. I have
problems in assigning probeset specific gene names as well as getting the
genomic coordinates. Furthermore I have no clue how to deal with the fact,
that most genes have
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
2007 Oct 30
6
trouble installing building packages from source using R 2.6.0 on Ubuntu Gutsy AMD64
I have recently upgraded to Ubuntu Gutsy and, for the first time, am
using a 64-bit installation. After failing miserably to install R from
source, not a problem for me in the past with a 32-bit install, I went
the route of using the Debian Etch build. This went smoothly, but I am
unable to update my numerous R and BioConductor packages, getting
non-zero exit status errors on each package. Is
2004 Oct 12
2
Why I can't retrieve GO identifier correctly?
Hello, R experts,
I tried to retrieve all biological process GO terms at level 3 starting
"biological process" as level 1 using the code as bellows:
1 library(GO)
2 library(GOstats)
3 level2<-getGOChildren("GO:0008150")$"GO:0008150"$Children
4 for ( i in 1:length(level2)) {
5 level3 <- getGOChildren(level2[i])$level2[i]$Children
6 for ( j in
2009 Dec 08
1
read.affy.mixed - subscript out of bounds error
Hello,
I have a problem with read.affy.mixed function. I want to read in
together a set of CEL files from chip types Affymettrix HGU133A_2 and
HGU133_Plus_2. I have my files to be read in in one directory together
with a white space delimited file describing them (covdesc). In this
directory I give a command:
> merge <- read.affy.mixed()
Error in merged[[i]] : subscript out of
2006 Sep 22
1
Possible bug in base::namespaceImportFrom?
Hi,
namespaceImportFrom in base/R/namespace.R has the following:
fdef <- methods:::getGeneric(genName, impenv)
The definition of getGeneric is in methods/R/RMethodUtils.R starts
with:
getGeneric <-
## return the definition of the function named f as a generic.
##
## If there is no definition, throws an error or returns
## NULL according to the value of
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