[R] out of colors in Mclust with 12 clusters

graphics grDevices datasets utils methods [8] base other attached packages: [1] lme4_0.99875-9 Matrix_0.999375-5lattice_0.17-6 [4] affy_1.17.9 preprocessCore_1.1.5 affyio_1.7.17 [7] Biobase_1.99.3 mclust_3.1-3 loaded via a namespace (and not attached): [1] grid_2

Re: [R] unix.time

see ?system.time Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 204-4202 Home (no voice mail please) mwkimpel

[R] 00LOCK error with site-library

pened with R-2.6.0, 2.6.1, and now with R-devel (2.7.0). If I have this setup incorrectly I am puzzled as to why it works with my local machine and why it worked with versions of R prior to 2.6.0. Ideas? Thanks, Mark -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana

Re: [R] 00LOCK error with site-library

Paul, Yes, I have manually removed it multiple times and it continues to reappear. I'll try to just upgrade a few packages at a time and see if there is one in particular that is causing the problem. Failing that, I'll run this past my system admin. Thanks for your help, Mark Mark

Re: [R] 00LOCK error with site-library

y [1] 0 #u unlink succeeds From the command line: ls -al drwxr-xr-x 3 mkimpel psych 4096 2007-12-11 23:13 00LOCK drwxr-xr-x 13 mkimpel psych 4096 2007-12-11 23:12 affxparser drwxr-xr-x 10 mkimpel psych 4096 2007-12-11 23:12 affyio Mark W. Kimpel MD *

[R] 64-bit package compilation problems on powerpc

IB.so] Error 1 My sysAdmin suggested removing the -mpowerpc64 bit flag if I encountered problems, but I though I would run this past our wizards to see if anyone had experience with this problem before recompiling. Mark -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana

Re: [R] best text editor for Linux?

-project.org/ There is a special help-list for ESS at: [EMAIL PROTECTED] Good Luck, Mark Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 204-4202 Home (

Re: [R] How to read HUGE data sets?

Depending on how many rows you will delete, and if you know in advance which ones they are, one approach is to use the "skip" argument of read.table. If you only need a fraction of the total number of rows this will save a lot of RAM. Mark Mark W. Kimpel MD ** Neuroinformatics *

[R] connectivity measure for graph nodes

. Thanks, Mark -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 204-4202 Home (no voice mail please) mwkimpelgmailcom _

[R] vertex labels in igraph from adjacency matrix

hat I am setting the vertex name attributes correctly? -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 204-4202 Home (no voice m

Re: [R] vertex labels in igraph from adjacency matrix

y use the C indexing convention, R users and their code, is much more in tune with indexing beginning at 1. Adjusting this in the R interface to igraph may solve many headaches down the road. Mark Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine

[R] confused about CORREP cor.LRtest

via a namespace (and not attached): [1] cluster_1.11.10 -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 204-4202 Home (no voic

[R] subset list based on logical within element flag

do this? Thanks, Mark > gene.pair.tf.lst [[1]] [[1]]$gene.pair [1] "Lgals1:Pxmp2" [[1]]$sig.cor [1] FALSE [[2]] [[2]]$gene.pair [1] "Lgals1:Pxmp2" [[2]]$sig.cor [1] TRUE [[3]] [[3]]$gene.pair [1] "Lgals1:Pxmp2" [[3]]$sig.cor [1] FALSE -- Mark W. Kimpe

Re: [R] sorting a data.frame by mean values of grouped data

d.lst.mn <- d.lst.mn[o] e <- NULL for (i in 1:length(d.lst.mn)){ if (i == 1){ e <- d[d$Group == names(d.lst.mn)[i],] } else { e <- rbind(e, d[as.character(d$Group) == names(d.lst.mn)[i],]) } } e Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana Universi

[R] fast way to compare two matrices of combinations

} if(!is.null(redundant.vec)){ triplets <- triplets[,-redundant.vec] count.vec <- count.vec[,-redundant.vec] } all.triplets <- cbind(all.triplets, triplets) all.count.vec <- c(all.count.vec, count.vec) } } } ##

Re: [R] fast way to compare two matrices of combinations

of order, and paste them together to make one unique string. Once I get something that works and is an optimized as I can make it, I'll post for future reference and for suggestions on further optimization. Mark Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University

[R] problem with merge

nDbi_1.1.26 RSQLite_0.6-8DBI_0.2-4 [19] graph_1.17.17limma_2.13.6 affy_1.17.9 [22] preprocessCore_1.1.5 affyio_1.7.15Biobase_1.99.2 loaded via a namespace (and not attached): [1] cluster_1.11.10 XML_1.93-2 Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana Univer

[R] 00LOCK error on site-library

tools_2.5.1 .Rprofile: .libPaths(new= "~/R_HOME/site-library") #tell R where site-library is -- --- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile &