similar to: how to map microarray probe to gene, homology

Un texte encapsul? et encod? dans un jeu de caract?res inconnu a ?t? nettoy?... Nom : non disponible URL : <https://stat.ethz.ch/pipermail/r-help/attachments/20110518/a7d31ce9/attachment.pl>

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!

Hello: I have looked at the bnlearn and deal packages for infering bayesian network. Can anyone suggest any other suitable package for constructing bayesian gene regulatory network using gene expression data? Thanks! John [[alternative HTML version deleted]]

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

I am running R 2.0.0, GOstats 1.1.1 and GO 1.7.0, and when I use the function GOHyperG, I have the following error: w1<-as.list(hgu95av2LOCUSID) w2<-unique(unlist(w1)) set.seed(123) myLL<-sample(w2,100) xx <- GOHyperG(myLL) Error in mget(x, env = GOTERM, ifnotfound = NA) : recursive default argument reference In fact first I tried this function with my locusId ' list (with

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

Hello All R-Gurus: ISSUE: Cannot view R vignettes due in Ubuntu Linux (a debian variant). note: this issue has been posted to this list before with no responses given see https://stat.ethz.ch/pipermail/r-help/2007-September/141178.html DETAILS: I am trying to view an R vignette. Here is the situation: I issue the openvignette(), then select the vignette I wish to view...and the system returns:

Are there any R packages to import and use Web Ontology Language (OWL) ontologies (represented in OWL/RDF or other form)? Thanks, -s [[alternative HTML version deleted]]

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. >

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

Hello, I've just started R, and I'm getting a bit mad using it. I've managed to produce a barplot with the labels for the ytick marks placed horizontally (perpendicular to the y-axis) usiing par(las=1). The problem is that most of my labels are in part beyond the plotting area because they are rather long (e.g. "H. sapiens", "D. melanogaster" ...). What is the

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

Hello: I have a 4-column dataset: Crime, Education, Urbanization, Age. I want to construct a multiple linear regression to find the effect of Education, Urbanization, and Age on Crime" lm(Crime ~ Education + Urbanization + Age) If I use + in above statement, does it mean it will build a model to find the relationship between Crime and Education when Urbanization and Age are held constant?

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

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

XLSolutions Corporation (www.xlsolutions-corp.com) is proud to announce: (1) Introduction to R/S+ programming: Microarrays Analysis and Bioconductor *** San Francisco / July 17-18, 2006 *** *** Chicago / July 24-25, 2006 *** *** Baltimore / July 27-28, 2006 *** *** Raleigh / July 17-18, 2006 *** ***

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

I would like to build a package for the HT HG-U133+ PM arrays from affy, but I can't find any good documentation on how to go about it. Naively using makecdfenv's make.cdf.package() causes R to seg-fault. I'm unfamiliar with the CDF format as such, but I'm guessing that it's changed somewhat because the PM arrays no longer have P/A and mismatches. I'm looking to build

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"

Hi, I am following the protocol outlined here for analysis of single channel Agilent microarray data: http://matticklab.com/index.php?title=Single_channel_analysis_of_Agilent_microarray_data_with_Limma I keep getting the following error message when using Limma's read.maimages function to load my data into an RGList object: Error in RG[[a]][, i] <- obj[, columns[[a]]] : number of