Mfuzz package
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dorothyc ▴ 140
@dorothyc-3150
Last seen 8.2 years ago
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
Clustering Mfuzz Clustering Mfuzz • 946 views
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@james-w-macdonald-5106
Last seen 1 hour ago
United States
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
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