search for: arabidopsi

Hi! I am trying to install the RMySQL package. The installation stops with the following error message. path to mysql is set. setenv PKG_CPPFLAGS /home/arabidopsis/software/R1.9.1/linux/mysql/include setenv PKG_LIBS /home/arabidopsis/software/R1.9.1/linux/mysql/lib R CMD INSTALL RMySQL_0.5-5.tar.gz #....cut cut. creating src/Makevars ** libs gcc -I/home/arabidopsis/software/R1.9.1/linux/lib/R/include /home/arabidopsis/software/R1.9.1/linux/mysql/include -I...

...nd added one additional line. The code runs beautifully if only complete cases are included and (though it builds the tree) breaks at the variable importance step missing data are presented. # From http://www.biomedcentral.com/content/supplementary/1471-2105-8-25-S1.R require("party") arabidopsis_url <- "http://www.biomedcentral.com/content/supplementary/1471-2105-5-132-S1.txt" arabidopsis <- read.table(arabidopsis_url, header = TRUE, sep = " ", na.string = "X") #arabidopsis <- subset(arabidopsis, complete.cases(arabidopsis...

Hello, I am beginner user of R. I am trying to use GeneNet package. I started by the example on this link: http://strimmerlab.org/software/genenet/download/arabidopsis-net.R However I am getting an error at this line:system("fdp -T svg -o arthdyn.svg arthdyn.dot") # SVG format sh: fdp: command not found I tried to search how to intall the fdp command but could not find explanation. I am running my code on Rstudio .95.263 and Mac OS X 10.6.8 Can you pl...

...One of those software packages is the AnnotationDbi package: it contains 41 package templates under inst/: [hpages at latitude Rpacks]$ ls AnnotationDbi/inst/AnnDbPkg-templates/ AFFYHUEX.DB CHIMP.DB MALARIA.DB WORM.DB ANOPHELES.DB COELICOLOR.DB MOUSECHIP.DB XENOPUSCHIP.DB ARABIDOPSISCHIP.DB ECOLICHIP.DB MOUSE.DB XENOPUS.DB ARABIDOPSIS.DB ECOLI.DB ORGANISM.DB YEASTCHIP.DB BASEPKG.DB FLYCHIP.DB PFAM.DB YEAST.DB BOVINECHIP.DB FLY.DB PIGCHIP.DB YEASTNCBI.DB BOVINE.DB GO.DB PIG.DB ZEBRAFISHCHIP.DB CA...

...o occur right after finishing the runforest() function in C and returning to R. I inserted the line: Rprintf("Done!\n"); as the last line of the runforest() function and got the following output: > library(randomForest, lib.loc="~/rlibs") > arabid <- read.table('arabidopsis.out', sep=' ', header=T) > arabid <- arabid[,-which(names(arabid) == "X0")] > set.seed(1) > fit <- randomForest(arabid[,-1], arabid[,1], ntree=100) > predict(fit, arabid[,-1]) Done! Program received signal SIGSEGV, Segmentation fault. 0x40152a48 in malloc (...

...Gentleman, > I am currently working on Streptomyces coelicolor microarray data. > > I have some clusters of genes and I would like to annotate them, but as you may know, this organism is not yet annotated with Gene Ontologies. There is no database (such as at "ath1121501.db" for Arabidopsis thaliana) available to use with the GOstats package. > > So, I would like to use at least the Kegg.db package with GOstats. > Can you tell me how to include KEGG.db ? I can't find anything about it. > > Thank you very much. > Roxane LEGAIE. > > > > > Roxa...

Hi - When I'm trying to read in a text file into a labeled character array, the memory stamp/footprint of R will exceed 4 gigs or more. I've seen this behavior on Mac OS X, Linux for AMD_64 and X86_64., and the R versions are 2.4, 2.4 and 2.2, respectively. So, it would seem that this is platform and R version independant. The file that I'm reading contains the upstream regions