[BioC] Mfuzz package

[James W. MacDonald]

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