similar to: problem with merge

Hello! I am crossposting this to R-help and BioC, since it is relevant to both groups. I wrote a wrapper for Entrez search utility (link for this is provided bellow), which can add some new search functionality to existing code in Bioconductor's package 'annotate'*. http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html Entrez search utuility returns a XML document

Dear all Does anybody know of updated Custom CDFs with binaries for MacOS. I'm trying to do affy-analysis using R-studio for Mac. Thanks Petter

Hi, I'm trying to calculate p-value to findout definitely expressed genes compare A to B situation. I got this data(this is a part of data) from whole organism , and each number means each expression values (that means, we could think 'a' gene is 13 in A situation, and it turns 30 in B situation) To findout probability, I'm going to use Audic - Claverie Method. ( The significance

I would like to track in which journals articles about a particular disease are being published. Creating a pubmed search is trivial. The search provides data but obviously not as an R dataframe. I can get the search to export the data as an xml feed and the xml package seems to be able to read it. xmlTreeParse("

Dear R folks: I am trying to use SSOAP (version 0.2-2) package in R (version 2.1.0,linux) to access SOAP service on NCBI (http://www.ncbi.nlm.nih.gov) its WSDL file is at http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl but some errors occured: > ncbi <- processWSDL("http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl") > ff <-

Hi dear Rers, I am using SSOAP package to access SOAP service at NCBI. I followed the example code in SSOAP but failed. > z <- .SOAP("http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/soap_adapter.cgi", method="run_eInfo", db="pubmed", action = I("einfo")) Error: protect(): protection stack overflow what's wrong? Thanks very much. Regards

Hi: I am trying to search PubMed abstracts which contains BOTH two terms: COL4A1 AND Ocular. I am using the following code: url= "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?" search = paste(url, "db=pubmed&term=COL4A1+AND+Ocular[abstract]&retmax=300", sep="") docId <- xmlTreeParse(getURL(paste(url, search, sep="")),

Hi: I am trying to query pubmed abstracts using the following syntax: url= "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?" search = paste(url, "db=pubmed&term=", queryTerm1, "+AND+", queryTerm2,"+OR+",queryTerm3, "+OR+", queryTerm4, "[abstract]&retmax=100&usehistory=y", sep="") docId <-

Hi, is there any package/function in Bioconductor that can do this: if given the chromosome positions of a fragment, find out all genes within, and with the information about which strand is the sense strand. And vice versa. Thanks a lot. ----- Appreciate your time & attention! -- View this message in context: http://www.nabble.com/list-genes-w-n-a-genomic-fragment-tp18331452p18331452.html

for the script, please kindly see the script below. At line 10 and line 13, my problems occurs. The first one is I try to retrieve the gene official name from a column of a table. The pattern of official name is something starting with gene_name. For detail problems, please see the according lines. Any suggestions are appreciated example of matching source (extract the Nnat, sometime it would

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

Hello! I am trying to get specific fields from an XML document and I am totally puzzled. I hope someone can help me. # URL URL<-"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=11877539,11822933,11871444&retmode=xml&rettype=citation" # download a XML file tmp <- xmlTreeParse(URL, isURL = TRUE) tmp <- xmlRoot(tmp) Now I want to extract only

Hello, Have anybody made tools for g-estimation (introduced by J. Robins) in R. http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=8235180&ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Regards, Jari Haukka

Hello R community, I am processing raw Affymetrix CEL files and I am using the Michigan custom CDF library hgu133plus2hsentrezgprobe. I have been looking for documentation on the function that it contains...I am specifically interested in converting probe names to gene symbols. Does anybody know where I can find it? Thank a lot! Eleni [[alternative HTML version deleted]]

Iam using R version 2.15 in a linux operating system. I have a matrix consisting of the gene ids and their specific signal intensity values as follows( a subset of the whole matrix) : probes GSM362180 GSM362181 GSM362188 GSM362189 GSM362192 244901 5.094871713 4.626623079 4.554272515 4.748604391 4.759221647 244902 5.194528083 4.985930299 4.817426064 5.151654407 4.838741605

Hi, I want to use reutils to obtain the accession numbers of a query search in character format. When I use efetch, the accession number isn't in a character format, and I'm not sure if the number is accurate, because I get the error: Error in file.exists(destfile) : object 'destfile' not found This is what I tried: UIDs<-esearch( "Methylation" ) accession_numbers

Hi All, I have an CBS segmentation algorithm output for 10 tumor samples each from 2 different tumors. Now, I am in an urgent need to assign gene (followed by all genes present) that belong to a particular segment after I removed all the CNVs from segment data. The format of the data is: Sample Chromosome Start End Num_Probes Segment_Mean Sample1A-TA 1 51598 76187 15

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

Duncan, you are a king! Thanks a lot for this cookie. It really helped me. Thanks for the code as well as detailed explanation at the end. >Hi Gregor. > >Here is a function that will collect all of the nodes in the >XML document whose names are in the vector elementNames > >getElements = >function(elementNames) >{ > els = list() > > startElement = function(node,

We are constructing growth charts (age/weight and age/length) for children with diagnosis that impacts weight/length. But we we don't know how to use R for producing growth charts. We are collection data of Age, Weight and Length. The data are used to produce diagnosis-specific Growth charts (like the CDC Growth Charts: