Hi, I'm trying out the Mfuzz package for soft clustering. I've encountered an error (please see below). I'd be really grateful if you could shed some light. > filename <- my_table > my.data <- read.table(filename, sep="\t") > set <-new("ExpressionSet", exprs = as.matrix(my.data)); > eset.r <- filter.NA(eset, thres = 0.25) 4 genes excluded. > eset.f <- fill.NA(eset.r, mode = "mean") > tmp <- filter.std(eset.f, min.std = 0) 1 genes excluded. > eset.s <- standardise(eset.f) > cl <- mfuzz(eset.s, c=6, m=2) Error in sample(1:xrows, ncenters) : cannot take a sample larger than the population when 'replace = FALSE' Thanks, Dorothy

Hi Dorothy, dorothyc wrote: > Hi, > > I'm trying out the Mfuzz package for soft clustering. I've encountered > an error (please see below). I'd be really grateful if you could shed > some light. > > > filename <- my_table > > my.data <- read.table(filename, sep="\t") > > set <-new("ExpressionSet", exprs = as.matrix(my.data)); > > eset.r <- filter.NA(eset, thres = 0.25) > 4 genes excluded. > > eset.f <- fill.NA(eset.r, mode = "mean") > > tmp <- filter.std(eset.f, min.std = 0) > 1 genes excluded. > > eset.s <- standardise(eset.f) > > cl <- mfuzz(eset.s, c=6, m=2) > Error in sample(1:xrows, ncenters) : > cannot take a sample larger than the population when 'replace = FALSE' How many microarrays do you have in eset.s? Best, Jim > > Thanks, > Dorothy > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826