Hint: Why do you think no one replied? 1. That it converged with one model/fitting algorithm and not with another is useless.
2. This cannot possibly be answered without your data. 3. A guess: you are overfitting -- glmnet regularizes and will therefore fit (highly) correlated regressors coxph won't. . -- Bert On Sat, Jul 6, 2013 at 5:04 AM, E Joffe <ejo...@hotmail.com> wrote: > Hello, > > > > [rephrasing and reposting of a previous question (that was not answered) > with new information] > > > > I have a dataset of 371 observations. > > When I run coxph with numeric variables it works fine. > > However, when I try to add factor (categorical) variables it returns "Ran > out of iterations and the model did not converge" > > > > Of note, when I restructure all factors to binary variables with dummy and > use glmnet-lasso the model converges. > > > > Here are examples of the code and output (including summary description of > the variables): > >> maxSTree.cox <- coxph (Surv(time,status)~Chemo_Simple, data=dataset) > > > > Warning message: > > In fitter(X, Y, strats, offset, init, control, weights = weights, : > > Ran out of iterations and did not converge > > > >> summary (dataset$Chemo_Simple) > > Anthra_HDAC Anthra_Plus ArsenicAtra > ATRA ATRA_GO > > 0 163 2 12 > 0 2 > > ATRA_IDA Demeth_HistoneDAC Flu_HDAC Flu_HDAC_plus > HDAC_Clof HDAC_only > > 0 34 37 4 > 24 1 > > HDAC_Plus LowArac LowDAC_Clof MYLO_IL11 > Phase1 > > 4 8 30 5 > 5 > > SCT StdARAC_Anthra StdAraC_Plus Targeted > VNP40101M > > 0 0 0 13 > 23 > > > > > > HELP !!!! > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
