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Hi, There is an excellent article at http://www.biomedcentral.com/1471-2105/9/307 by Stroble, et al. describing variable importance in random forests. Does anyone have any suggestions (besides imputation or removal of cases) for how to deal with data that *have* missing data for predictor variables? Below is an excerpt of some code referenced in the article...

...e(m) I need to generate a Venn diagram from this data.frame, displaying the various intersections of 'yes' for the different columns. Ideally, the circle for each column should be proportional to the number of non-NA entries. The package "VennDiagram" (described here: http://www.biomedcentral.com/1471-2105/12/35) can do all this. However, I have not been able to figure out how to transform the data.frame into the required list format. Any suggestions on how to do this? Many thanks, Lara

Hello, I am looking for a sample size function for samples sizes, to test proportions that are not binomial proportions. The proportions represent a ratio of (final measure) / (baseline measure) on the same experimental unit. Searches using RSeek and such bring multiple hits for binomial proportions, but that doesn't seem to fit my situation. Perhaps there's some standard terminology

...ing Tukey's HSD method. I would like to plot the data as boxplots or dotplots, with horizontal significance lines indicating which groups are statistically significantly different, according to Tukey HSD. Here's a nice image showing an example of such a graphical display: http://www.biomedcentral.com/1471-2148/11/99/figure/F2 Is there a R function for this? I have tried searching, and found several nice plotting fuctions for Tukey's HSD, but they all either hide the actual data, or display the results only with letters indicating (non-)signifiance. Examples: # Fit an one-way ANOVA...

Gene names being misinterpreted by spreadsheet software (read.csv is no different) is a classic issue in bioinformatics. It seems like every practitioner ends up encountering this issue in due time. E.g. https://pubmed.ncbi.nlm.nih.gov/15214961/ https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1044-7 https://www.nature.com/articles/d41586-021-02211-4 https://www.theverge.com/2020/8/6/21355674/human-genes-rename-microsoft-excel-misreading-dates On Tue, Apr 16, 2024 at 3:46?AM jing hua zhao <jinghuazhao at hotmail.com> wrote: > > Dear R-devel...

Dear list, If I know the standard error for k1 and k2, is there anything I can call in R to calculate the standard error of k1/k2? Thanks. Jun [[alternative HTML version deleted]]

Hello, I'm an MD working in an eye clinic. I'm learning by myself to use R for use in my research works and for implementation in a software project. There are some authors who recomends the use of Cox regression as a substitute for Logistic regression (<a href="http://www.biomedcentral.com/1471-2288/3/21.pdf"> Barros AJD, Hirakata VN. BMCMedical Research Methodology, 2003; 3:21 </a>. The use of Cox regression permit the estimation of the prevalence rates rather than Odds ratios obtained by logistic regression analysis. Cox regression is used for time-to-event data....

Dear R User, Please, I am new to R. I want to overlay density plot for predictive interval pooled result in meta-analysis. http://addictedtor.free.fr/graphiques/graphcode.php?graph=114 Regards Frank Peter

...Lasso, adaptive Lasso and Ridge Regression. More details can be found in the accompanying article Nicole Kr?mer, Juliane Sch?fer, Anne-Laure Boulesteix. Regularized Estimation of Large Scale Gene Association Networks using Gaussian Graphical Models BMC Bioinformatics, 10:384, 2009. http://www.biomedcentral.com/1471-2105/10/384 Please send an email to nkraemer at cs.tu-berlin.de for any comments, suggestions, or bug reports. Best regards, Nicole & Juliane -- Dr. Nicole Kr?mer TU Berlin Machine Learning/Intelligent Data Analysis fon: (+49) 30 314 78627 Franklinstr. 28/29, 10587 Berlin, German...

...email carefully. It explains what has happened to your email, which suspected virus has been caught and what to do if you need help addressing the problem. To help identify the quarantined email: The message sender was r-help at lists.r-project.org The message recipients were info at biomedcentral.com The message title was Your details The message date was Tue, 19 Aug 2003 12:57:34 +0200 The virus or unauthorised code identified in the email is /var/qmail/queue/split/1/attach/570489_2X_PM4_EMS_MA-OCTET=2DSTREAM__movie0045.pif Found the W32/Sobig.f at MM virus !!! Some viruses for...

...Lasso, adaptive Lasso and Ridge Regression. More details can be found in the accompanying article Nicole Kr?mer, Juliane Sch?fer, Anne-Laure Boulesteix. Regularized Estimation of Large Scale Gene Association Networks using Gaussian Graphical Models BMC Bioinformatics, 10:384, 2009. http://www.biomedcentral.com/1471-2105/10/384 Please send an email to nkraemer at cs.tu-berlin.de for any comments, suggestions, or bug reports. Best regards, Nicole & Juliane -- Dr. Nicole Kr?mer TU Berlin Machine Learning/Intelligent Data Analysis fon: (+49) 30 314 78627 Franklinstr. 28/29, 10587 Berlin, German...

Dear R-users, I build already many contour graphs using the contour-procedure in R (akima library), after interpollating my data z on x,y (see e.g. graphs in this paper: http://www.biomedcentral.com/content/pdf/1471-2148-9-16.pdf). Now, however, i experience unexpected and completely unsensible problems: after building the syntax, i can create the graphs and use the interp-command without any problems. However, after shutting down R and opening the saved syntax (that worked), i now get th...

...o que el de ROC estática): - el paquete survivalROC http://cran.r-project.org/web/packages/survivalROC/survivalROC.pdf - y risksetROC http://cran.r-project.org/web/packages/risksetROC/risksetROC.pdf El siguiente artículo sobre pROC está muy bien para ver las capacidades de la librería: http://www.biomedcentral.com/1471-2105/12/77 #### con tus datos # Pon tu directorio de trabajo setwd("C:/Users/pedroc/Downloads") list.files() # Lees el fichero, ojo al separador decimal rocdata <- read.table(file = "roc.csv", header = T, sep = ";&q...

??Gracias Javier,? 2017-04-01 12:07 GMT-03:00 <javier.ruben.marcuzzi en gmail.com>: > Mi duda es la siguiente, la varianza residual en su modelo, es homogénea o > heterogénea, ?La varianza es homogénea, común a todas las observaciones. Digamos que el modelo es el siguiente, y=f(x, betas)+e con f alguna función no lineal cuyos parámetros son betas y con e~N(0, sigma2). Uno suele

Hello, I am trying to explore the use of random forests for classification and am certain about the interpretation of the importance measurements. When having the option "importance = T" in the randomForest call, the resulting 'importance' element matrix has four columns with the following headings: 0 - mean raw importance score of variable x for class 0 (where

Dear R-developers, I came to a somewhat unexpected behaviour of read.csv() which is trivial but worthwhile to note -- my data involves a protein named "1433E" but to save space I drop the quote so it becomes, Gene,SNP,prot,log10p YWHAE,13:62129097_C_T,1433E,7.35 YWHAE,4:72617557_T_TA,1433E,7.73 Both read.cv() and readr::read_csv() consider prot(ein) name as (possibly confused by

...23 > http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1121605/pdf/1123.pdf > > > The use of percentage change from baseline as an outcome in > a controlled trial is statistically inefficient: a > simulation study. > Vickers AJ. > BMC Med Res Methodol 2001;1:6. > http://www.biomedcentral.com/1471-2288/1/6 > http://www.biomedcentral.com/content/pdf/1471-2288-1-6.pdf > > > and review an additional web site: > > ? http://biostat.mc.vanderbilt.edu/wiki/Main/MeasureChange > > > Once you are hopefully in a position of adopting a > regression based appro...