Federico Giorgi

Hi there! Thanks for using ARACNe-AP. To convert the ARACNe-AP into an R object, this is what we used to do. Assuming all the outputs of ARACNe-AP are saved as files 3col.gz Loading code: library(viper) library(mixtools) Necessary functions: aracne2regulon<-function(afile, eset) { dset <- eset annot <- rownames(eset) names(annot) <- rownames(eset) rm(eset) tmp <- as.matrix(read.delim(afile,as.is=TRUE,header=TRUE)[,1:3]) aracne <- data.frame(tf=tmp[, 1], target=tmp[, 2], mi=as.numeric(tmp[, 3])/max(as.numeric(tmp[,...

Hi Juan! This implementation of aracne is to be run directly as a jar file from the command line. E.g. java -jar Aracne.jar Try to run some of the examples in the wiki from the command line (from the Windows command prompt or the Ubuntu terminal, for example).

Hi Juan! Aracne-geWrokbench is not maintained by us, you should contact Aristidis Floratos at Columbia University for it. As an alternative, you can use our Aracne-AP, which doesn't require a microarray name to run!

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