similar to: G-estimation in R?

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

Hello All, While trying to install Matrix package following error message came out: /usr/bin/ld: cannot find -lblas-3 collect2: ld returned 1 exit status make: *** [Matrix.so] Error 1 ERROR: compilation failed for package 'Matrix' ** Removing '/usr/lib/R/library/Matrix' ** Restoring previous '/usr/lib/R/library/Matrix' It seems that someting is missing. Have anybody

Hello, Has anyone written R functions for applying self-controlled case series methods (http://statistics.open.ac.uk/sccs/). In fact only thing needed is to modify glm function to allow absorption of effect. Eg. in Poisson model individual effect is used as factor, but it is considered as nuisance term where parameter estimates are not needed. Could anyone point how absorbing individual

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

I have used merge regularly and thought I understood how it worked, but I must not. I have two dataframes with identical colnames from two different experiments, TL01 and LC01. Each dataframe has a column named "Entrez.Gene", which I have converted to "as.character" just to make sure merge is not looking at factor levels. Because I have done some filtering, the Entrez.Gene

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

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 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 <-

http://bass.directhit.com/openssh_snap/ Starting tonight I plan on tracking changes very closely with the OpenBSD tree. I need people to test the latest snapshot (9/14 at of right now) and report success or failure on compiling. I am starting this now because we are looking at a code freeze soon and I really want to ensure it compiles and runs on all existing platforms. So we (the portable

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

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,

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

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("

Hi R users I try to use the lme but I can?t!!!!! My script is (some words in french, sorry!!): rm(list=ls(all=TRUE)) #Efface tous les objets en m?moire pour ?viter des erreurs library(MASS) #Chargement des Librairies library(car) library(Hmisc) library(tkWidgets) library(svDialogs) library(multtest) library(nlme) #Rep <- "C:/Documents and Settings/U3M/Bureau/steph/Scripts

I've just installed wget so that I could get new packages, but when I try to use it, it just tries to get the connection cran.r-project.org:80... My computer uses Windows NT system and internet connections go through port 8080 so I think there's the problem, but how to change it? I've tried to set packages through MS DOS, but that doesn't work either, because make libR.a says

Hi, This is a very basic question, but apparently I am too stupid for it. I have a large matrix A, and I need to avoid for loops. How could I apply a function f(a,r,c) on each element of A, using the subscript (row and column) of a as the other arguments? Thanks in advance, Markku Karhunen National Public Health Institute, Finland

Full_Name: Jussi Jousimo Version: 2.1.1 OS: Linux Submission from: (NULL) (193.167.195.60) R 2.1.1 crashes when it is trying to write a file with the postscript driver to a directory, where the user has no permission to write. For example, postscript("foo.ps") gives an error message: *** glibc detected *** free(): invalid pointer: 0x08a469b0 ***. The problem is at the PSDeviceDriver

Full_Name: Jussi Jousimo Version: 2.2.0 beta OS: Windows XP Submission from: (NULL) (193.167.195.60) I'm trying to assign a zero length vector to a list: x<-numeric() length(x) foo<-list() foo$bar[[1]]<-x length(foo$bar[[1]]) foo But in the list this vector turns out to be length one with random content. x<-character() makes R to crash.