similar to: graphlets -- more

I've been experimenting some with the graphlets which S-Plus 6.1 has. Is there something similar in R? I've looked through documentations, and at SJava, but haven't found it. (If you don't know what a graphlet is, here's what it appears to be: a graphlet is a binary file that encodes information about a graph. Java uses spgraph.jar to display the graph and allow certain

Naras presented something with similar functionalities using SVG a couple of years ago, and since then the svgdevice package had been made available. I do not know SVG myself, but according to Naras, it's all possible. Best, Andy From: Terry Therneau > > I have an application where the Splus graphlets() package > would work very well, and would like to know if there is any

Hi all, I have created my network using igraph package. It provides graphlet function to calculate number of graphltes. I want to find graphlet degree distribution agreement of a graph. How can i achieve that..?? The package ergm.graphlets is there in r but there isn't any examples available for usage of this package. My R script is: library(igraph) g2 <- graph.formula(A:B - A:C, X:Z -

Hi dear R-listers, I'm trying to fit a 3-level model using lme in R. My sample size is about 2965 and 3 factors: year (5 levels), ssize (4 levels), condition (2 levels). When I issue the following command: > lme(var~year*ssize*condition,random=~ssize+condition|subject,data=smp,method ="ML") I got the following error: Error in logLik.lmeStructInt(lmeSt, lmePars) :

I know that there are quite a few packages out that there for cluster analysis. The problem that I am facing is finding a package that will not incorporate all my samples into clusters but just the samples that fit a threshold (that I have not set yet and may need help finding the right level) for genotyping. It should be able to "no call" samples outside the clusters. It also needs to

Hello R-devel, I am currently attempting to implement an API similar to data.table wherein single bracket subsetting can accept an unquoted expression to be evaluated in the context of my object. A simple example from the data.table package looks like this: DT <- data.table(col1 = c('a', 'b', 'c'), col2 = c('x', 'y', 'z')) DT[col1 ==

I've created some Splus code for a microarray problem that - needed to be in C, to take advantage of some sparse matrix properties - uses a cholesky decompostion as part of the computation For the cholesky, I used the cholesky2 routine, which is a part of the survival library. It does just what I want and I'm familiar with it (after all, I wrote it). In Splus, this all works

This is my first post requesting help to this mailing list. I am new to R. My apologies for any breach in posting etiquette. I am new to this language and just learning my way around. I am attempting to run some sample code and and am confused by the error message: Loading required package: rrcov Error in fitNorm2(fdat[, "FSC-H"], fdat[, "SSC-H"], scalefac = ScaleFactor) :

Greetings ~ I need some assistance determining an appropriate approach to analyzing multivariate binary response data, and how to do it in R. The setting: Data from an assay, wherein 6-hours-post-fertilization zebrafish embryos (n=20, say) are exposed in a vial to a chemical (replicated 3 times, say), and 5 days later observed for the presence/absence (1/0) of defects in several organ systems

For any given pre-specified gene or short list of genes, yes the Cox model works fine. Two important caveats: 1. Remeber the rule of thumb for a Cox model of 20 events per variable (not n=20). Many microarray studies will have very marginal sample size. 2. If you are looking at many genes then a completely different strategy is required. There is a large and growing literature; I like Newton

Hi I have been trying to get the R Extention supportware going for a while now and have been running to an error I cannot figure out. I am hoping someone here will recognize whats going on and what i may be messing up. After installing all the components - Rtools, Active Perl, and minGW I created the file structure using package.skeleton(name = "test") with only the functions i want

Hi I am still trying to wrap up a package using Rcmd (in windows 2000 professional with R 1.8.1). I have made some progress - and now at least Rcmd check works - it still giving me an error message when it creates latex help files though. Thus I get: c:\rpack> Rcmd check test * checking for working latex ... OK * using log directory 'C:/rpacks/test.Rcheck' * checking for file

Hi. I have data which i would want to assess the degree of agreement between two assays, e.g., to evaluate reproducibility or for inter-rater reliability. I have used the Pearson product-moment correlation coefficient. It looks good ranginging between 0.90 to 0.998. Though this looks good. I am told the Concordance correlation coefficient will give a better picture of how reproducible the assay

Hello R-Members I have to install several R packages on a Unix server which doesn't have internet connection. I downloaded some packages manually and I installed it from source using the command R CMD INSTALL and it's work but in some cases I can't install the package because of the dependencies. So I download all the R packages into a directory for example /home/joel/RPacks.

Dear listers, After activating the name space for my bioconductor package (prada) I successfully ran R CMD check. However when loading the package in R and running the examples the imported function brewer.pal from package RColorBrewer is not found. I can directly call brewer.pal from the RColorBrewer name space typing RColorBrewer::brewer.pal, but it is not imported into my prada name space. When

Dear listers, After activating the name space for my bioconductor package (prada) I successfully ran R CMD check. However when loading the package in R and running the examples the imported function brewer.pal from package RColorBrewer is not found. I can directly call brewer.pal from the RColorBrewer name space typing RColorBrewer::brewer.pal, but it is not imported into my prada name space. When

Dear R-helpers, I am developing a Mixed-Effects model for a study of immunoassays using 'lme4' library. The study design is as follows: 10 samples were run using 7 different immunoassays, 3 times each, in duplicates. Data attached. I have developed the following model: c.lme <- lmer(Result~SPL + (SPL|Assay/Run) -1, data=data) This model has excellent predictions - the Rsquared of

Rich, Thank you for the very quick response. I tried the echo command that you listed and it still gives me the same error: Any other possible suggestions? On Monday, October 5, 2020, 02:42:08 PM EDT, Richard W.M. Jones <rjones@redhat.com> wrote: On Mon, Oct 05, 2020 at 06:28:06PM +0000, Alexander Prada wrote: > Here is my output I am getting on my kali machine. I believe

Hi, I have a script that takes a subset of genes on a microarray and tries to fit a coxph model to the expression values for each gene. This seems to work fine but in some cases it produces warnings and/or errors. For example: Error in fitter(X, Y, strats, offset, init, control, weights = weights, : NA/NaN/Inf in foreign function call (arg 6) In addition: Warning message: In fitter(X, Y,

Dear all, Is there anyway too generate MA plot for 2 qPCR assays (an array of 2x 400). -- View this message in context: http://r.789695.n4.nabble.com/Bioconductor-MA-plot-for-qPCR-array-tp4182805p4182805.html Sent from the R help mailing list archive at Nabble.com.