Displaying 20 results from an estimated 700 matches similar to: "Query Gene ontology"
2002 Dec 18
2
gene ontology association
Hello! I don't know if there is some R-package able
to associate ontology to a long list of GeneBank Name (a txt-tab file or
an XML file), i.e.
I would as output a formatted file with 4 columns (1:GeneBank Name
2,3,4:ontology).
I know that I have to perform a mapping of genes, I got a look on
AnnBuilder pkg,
but I 've not idea from where to start.
Some suggestion? Thanks in advance!
2010 Oct 11
1
Response to your LC Comment -2393 on Media Ontology spec
Dear Jean-Marc:
Would you please send Thierry an ontology mapping table specification
for speex according to the format he links to at the end of his
message below? Thank you.
On Mon, Oct 11, 2010 at 9:54 AM, Thierry MICHEL <tmichel at w3.org> wrote:
> Dear James,
>
> In your latest email to the MAWG response to your comment, you seem to
> disagree with the MAWG proposal.
>
2002 Jan 21
1
[R-1.4.0] minimum spanning tree of large ontology
Dear all,
I have an ontology which I would like to load in R to then compute the
minimum distance between elements.
Since this ontology is not only DAG, the problem is non trivial and
therefore decided to use R with the powerful e1071
library (allShortestPaths) to do that. That method requires to provide a
distance matrix between the
various objects. My ontology contains 32768 objects and
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
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2008 May 05
1
computational ontology to research questions, and statistical methods
our group at Duke is currently attempting to connect two data sets fed
through a web-based system, one containing research questions (i.e.,
variables positioned with certain roles) and a database of statistical
methods. this connection is done informally in a number of R packages
and related software such as Rcmdr, R4calc, and Rkward where a
variable of a certain type is matched to a certain
2010 Jun 10
1
OWL ontologies in R?
Are there any R packages to import and use Web Ontology Language (OWL)
ontologies (represented in OWL/RDF or other form)?
Thanks,
-s
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2006 Sep 06
1
Help on estimated variance in lme4
Dear all,
I get an error message when I run my model and I am not sure what to do
about it.
I try to determine what factors influence the survival of voles. I use a
mixed-model because I have several voles per site (varying from 2 to 19
voles).
Here is the model:
###
fm5 <-lmer(data=cdrgsaou2,
alive~factor(pacut)+factor(agecamp)+factor(sex)+ResCondCorp+(1|factor(cdrgsa
ou2$ids)),
2007 Nov 06
1
R crashes when I open R files in R (PR#10402)
Full_Name: Jerome Lemaitre
Version: 2.6.0
OS: Windows XP
Submission from: (NULL) (132.203.202.117)
Hello,
I have recently downloaded the 2.6.0 version of R and I experience troubles that
never happened to me with previous versions.
I open an R session with an R shortcut in "My documents/Analyses". However, when
I want to open R files such script using "File/open script" R
2008 Nov 16
3
[Schrodinger-devel] ogg dirac granulepos in oggz tools
On 11/14/08, David Flynn <davidf+nntp at woaf.net> wrote:
> Correct; there is no metadata handling capability in the current
> mapping spec.
I'd suggest at some point to look into separate stream solution for
metadata, perhaps M3F [1].
-Ivo
[1] http://wiki.xiph.org/index.php/M3F
2006 Jan 20
4
read.table with ":" in column names (PR#8511)
Full_Name: emiel ver loren
Version: 2.2.0
OS: Windows XP
Submission from: (NULL) (145.117.31.248)
Dear R-community and developers,
I have been trying to read in a tab delimeted file where the column names and
the row names are of the form "GO:0000051" (gene ontology IDs). When using:
> gomat<-read.table("test.txt")
> colnames(gomat)[1]
[1] "GO.0000051"
2009 Dec 24
1
Question to use R plot GO pie chart
Hi,
I have a list of IPI gene IDs. I want to find out whether there is a
package which can map the gene ontology to these IPIs, and plot the
pie chart to demonstrate the molecular function distributions.
The input is like the following gene IPI IDs:
IPI:IPI00008860.1|SWISS-PROT:Q9BXJ4-1|TREMBL:Q542Y2|ENSEMBL:ENSP00000231338;EN
2006 Aug 30
8
converting decimal - hexadecimal
Hi,
do you know, a method to convert an decimal value (integer) to the
corresponding hexadecimal value ?
thinks for help.
Romain
--
Lorrilli?re Romain
UMR 8079 Laboratoire Ecologie, Syst?matique et Evolution
B?t. 362
Universit? Paris-Sud
91405 Orsay cedex
France
tel : 01 69 15 56 85
fax : 01 69 15 56 96
mobile : 06 81 70 90 70
email : romain.lorrilliere at ese.u-psud.fr
2013 May 03
1
MANOVA summary.manova(m) :" residuals have rank"
Dear All, I am trying to perform MANOVA. I have table with 504 columns(species) and 36 rows) with two grouping (season and location)
Zx <- Z[c(4:504)]
Zxm <- as.matrix(Z)
m<- manova(Zxm~Season*location, data=Z)
when I do summary.aov, I get respond for each species but summary.manova
summary.manova(m) :" residuals have rank" 24<501.
What can it be the reason for this error
2012 Mar 13
7
ROC Analysis
Hi everybody,
I have a data set with a value and a status (positive or negative case) and
I want make a ROC Analysis. So, with ROCR Package, I have got the ROC curve
(True Positive Fraction [tpf] according 1-True Negative Fraction [1-tnf]).
http://r.789695.n4.nabble.com/file/n4469203/01.png
But, now I want a new graphic which show the sum of true positive fraction
and true negative fraction
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
2013 Jul 12
3
Needing help for excluding vector elements
Hello,
R for Dummies.
How can I exclude the first 1000 values of a vector (length 12000)? More
generally all the values up to the ith?
Thanks for your help,
Dr Olivier Charansonney
Cardiologue
Centre Hospitalier Sud-Francilien, Corbeil-Essonnes, France
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2010 Aug 25
1
SEM : Warning : Could not compute QR decomposition of Hessian
Hi useRs,
I'm trying for the first time to use a sem. The model finally runs,
but gives a warning saying :
"In sem.default(ram = ram, S = S, N = N, param.names = pars, var.names
= vars, : Could not compute QR decomposition of Hessian.
Optimization probably did not converge. "
I found in R-help some posts on this warning, but my attemps to modify
the code didn't change
2008 Apr 10
3
option_groups_from_collection_for_select with a ActiveRecord::Base single object
Rails documentation gives examples of using
option_groups_from_collection_for_select with two tables/objects.
How could it be done with one?
Example that almost works:
I have a form to enter address from both the United States and Canada.
It has the following:
====new.html.erb====
<%= select_tag(
:state,
option_groups_from_collection_for_select(
State.countries,
:country,
2008 Nov 03
1
Help with 'annotation' in GOHyperGParamsClass
Dear cateGOry experts,
hyperGTest documentation states that YEAST cannot be used as 'annotation'
when evaluating gene ontology representation status for a given set of
'geneIds'.
Because I am using a custom print I believe I need to create my own data
package to use as the annotation file for 'annotation'. Can someone please
describe how to make a data package that will
2012 Nov 22
2
Trick to replace NA
Dear members,
I have a series of values in a vector and some value are missing and
replaced with NA.
For example:
a <- c(27, 25, NA, NA, 24, 26, 27, NA, 26)
I would like to replace the NAs with the value taken from the previous
value that is non-NA. The output would be in this case:
27 25 25 25 24 26 27 27 26
Now I do that with a for loop, but I try to eliminate all the loops to
gain in