search for: cancer

...answer with a single (or two) commands with the right extensions, but I really can't figure this out right now. I have several hundred pheno factors actually, so manually doing this line by line is not an option. My original table is approximately like this : ID pheno 1 A Breast Cancer 2 A Appendicitis 3 A Microcephaly 4 B Polyps 5 B Autism 6 C Autism 7 D Breast Cancer 8 D Polyps 9 D Appendicitis 10 E Breast Cancer What I want is this : ID Breast Cancer Appendicitis Microcephaly Polyps Autism A 1 1 1 B 1 1 C 1 D 1 1...

Head of Department of Applied Statistics and Epidemiology - Institute of Cancer Epidemiology, Copenhagen, Denmark The Institute Population-based cancer research in the Nordic countries is in the international forefront. Since the foundation of the Danish Cancer Registry in 1942 the Institute of Cancer Epidemiology has played a significant role in this research area. The...

...ce value for each of predictions type (linear predictor, risk and terms) is the mean covariate within strata. If the psline is specified for the covariate, what's the reference value for the predictions? I did some test code below: ### par(mfrow = c(1,3)) test = coxph(Surv(time, status) ~ age, cancer) test2 = coxph(Surv(time, status) ~ pspline(age, df=2), cancer) test3 = coxph(Surv(time, status) ~ pspline(age, df=5), cancer) pptest3=predict(test3, type="lp") pptest2= predict(test2, type="lp") pptest = predict(test, type="lp") plot(cancer$age, exp(pptest)) abline(v=...

I want to do a logistic regression without an intercept term. This option is absent from glm, though present in some of the inner functions glm uses. I gather glm is the standard way to do logistic regression in R. Hoping it would be passed in, I said > r <- glm(brain.cancer~epilepsy+other.cancer, c3, > family=binomial(link="logit"), intercept=FALSE) which produced Error in glm.control(...) : unused argument(s) (intercept ...) Is there an easy way to do this? I suppose I could start hacking away at glm so it would take the argument and pass it on...

Dear all, we have an exciting PhD position applying HPC to the analysis of large scale cancer datasets. The post will suit an applicant from a strong computational background who wishes to apply their knowledge to help develop a better understanding of the processes that control how tumours develop. Details below:- High Performance Computing applied to cancer research: Computational anal...

COMPUTATIONAL ANALYSIS OF NEXT GENERATION SEQUENCE DATA (http://bioinformatics.nki.nl/vacancies.php) THREE BIOINFORMATICS POSITIONS PROJECT OUTLINE Genomic alterations are major determinant of responses to (targeted) therapies in cancer. In fact, the best positive and negative predictors of responses to targeted therapies are alterations in kinases or their direct downstream effectors. To gain insight into resistance mechanisms to therapy and thus better tailor treatment, we are approaching this problem from two different angles....

...positions in and around bioinformatics, biostatistics and computational biology. These range from HPC and mathematical programming, through biostatistics and biomarkers, to computational biology and bioinformatics. Focuses include single cell genomics and personalised medicine in lung and prostate cancer. For full details, please visit our website at: http://www.cruk.manchester.ac.uk Brief summaries below: RNA Biology Group - Crispin Miller ========================== Postdoctoral Scientist in Computational Biology: A position is now available for a highly motivated postdoctoral research scienti...

  Hello to everyone, I am new to programming in R and am having trouble with the following two commands 1.I am running a simple 1 line script "read.table(file="C:\\Document and Settings\\All Users\\Desktop\\colon cancer.txt) and the error message I get is "Error in file (file, "r"): cannot open the connection In addition warning message In file (file, "r"): cannot open file'C:\Document and Settings\All Users\Desktop\colon cancer..txt   2.I am running the simple 1 line script print (fi...

Systems Analyst /Programmer III/IV (AD-22564) About Us Fred Hutchinson Cancer Research Center, home of three Nobel laureates, is an independent, nonprofit research institution dedicated to the development and advancement of biomedical research to eliminate cancer and other potentially fatal diseases. Recognized internationally for its pioneering work in bone-marrow transplan...

Dear UseRs, Suppose I have data regarding smoking habits of a prospective cohort and wish to determine the risk ratio of colorectal cancer in the smokers compared to the non-smokers. What do I do at the end of the study with people who die of heart disease? Can I just censor them exactly the same as people who become uncontactable or who die in a plane crash? If not, why not? I'm thinking that heart disease isn't independen...

dear all, I am a student in cs college. I would like to know how to plot infinte number of genes after using the svm. the data set i have consists of x which is a matrix of 39 cancer patients [rows] and 2000 gene names [colmns]. each cell is the value of the gene for a particular patient. there are two types of cancer people representedas factor y. here is the code: library(e1071) #load database db <- read.csv(file="databases\\colon-cancer\\colon-cancer.csv",hea...

Hi! I would like to select probes (affy expression set) of genes that are "cancer-related". Conventionally the decision whether a gene is cancer-related or not is made by looking up the literature. Since this is not possible for all genes on the array I wonder if there is a way of doing this automatically? Best wishes Kristian -- _____ Dr Kristian Unger Imperial Co...

...Relative survival and the package splinesurv<http://cran.r-project.org/web/packages/splinesurv/index.html> is for Nonparametric bayesian survival analysis. (For your information, relative survival is the method of choice for estimating patient survival using data collected by population-based cancer registries although its utility is not restricted to studying cancer( Dickman and Adami 2006; Dickman et al. 2004).”, which is a concept defined by Berkson (1942) and Berkson & Gage (1950).Two data files are required in order to estimate relative survival; a file containing individual-level dat...

The Gottardo lab at the Fred Hutchinson Cancer Research Center in Seattle has an opening for a programmer. To apply: https://erecruit.fhcrc.org/psp/RECRUIT/EMPLOYEE/HRMS/c/HRS_HRAM.HRS_CE.GBL?Page=HRS_CE_JOB_DTL&Action=A&JobOpeningId=24122&SiteId=2&PostingSeq=1 The position description is below: About Us Fred Hutchinson Ca...

...my loglikelihood by writing a function directly for loglikelihood and try to optimise using optim it gives warnings as well as error and if i use NLMINB then convergence is false. Can someone save my soul..... pl!!!!!!!!z below is my program script .............. #ovarian cancer data and parity among 769 probands and their mothers #cancer in proband y1<-c(1,1,1,1,1,1,1,rep(1,29),rep(1,36),rep(1,41),r! ep(1,85),rep(1,105),rep(1,84), 1,rep(0,22),rep(0,33),rep(0,38),rep(0,50),rep(0,103),rep(0,135)) #cancer in mother y2<-c(1,1,1,1,1,1,1,rep(0,29),r...

I had the latest wine running under winblows 98 SE for a week or two with no problems, then I installed winblows 2000 and now I cannot get wine to work. It is important for me to get it running again since I run United Devices cancer research agent (http://members.ud.com) 24/7 to help them find a cure for cancer. Is wine compatible with Win2k, or will I need to re-install 98 again? -- Interested in finding a cure for cancer? http://members.ud.com/services/teams/team.htm?id=2910655E-026A-47F8-A1CE-C45 B9BAAB072-

Dear Asterisk Community, Does your company provide inbound 800# origination? If so, please read this message and e-mail us a quote for monthly co-lo hosting of our asterisk server and per-minute inbound 800# origination. The Prostate Cancer Research and Education Foundation (PC-REF) is a non-profit organization dedicated to helping prostate cancer sufferers and their loved ones. We have created a weekly "call-in show" using Asterisk that we offer as a FREE service to the public. Callers can ask their questions from world r...

Hi everyone, I connected a data in FileMaker server with odbcConnect. When I call the data "CANCERS" using sqlFetch, it looks okay. However, the number of obs was different with the actual number. If I read the same data from Microsoft Access, there are 656 obs. in it but srt() shows me 600 obs. Does anyone know why this happened and how to read all obs. from R? Thank you in advance. EJ...

Dear fellow R-help members, I hope to seek your advice on how to parse/manage a dataset with hundreds of columns. Two examples of these columns, 'cancer.problems', and 'neuro.problems' are depicted below. Essentially, I need to parse this into a useful dataset, and unfortunately, I am not familiar with perl or any such language. data <- data.frame(id=c(1:10)) data$cancer.problems <- c("Y; DX AGE: 28; COLON", "&quot...

I am looking for an online (easily accessible) form of the samples of genetic data for those with cancer and those without cancer. Can anyone direct me in the right place? Thanks, Jim [[alternative HTML version deleted]]