[BioC] [Mfuzz] Error in cmeans(exprs(eset)

[Maciej Jończyk]

Dear List Members,

I use Mfuzz package. I've successfully clustered two data sets.
I wanted to cluster third data set (very similar to those two)
and I encountered following error in both cselection and partcoef:


> roznice=read.table("allstop",header=T,row.names=1,sep="\t")
> rozn_set=new("ExpressionSet",exprs=as.matrix(roznice))
> dim(roznSR)
Features  Samples
     902        7
> class(rozn_set)
[1] "ExpressionSet"
attr(,"package")
[1] "Biobase"
> roznS=standardise(rozn_set)
> roznSR=randomise(roznS)
x=cselection(roznSR,m=1.25,crange=seq(4,40,1),repeats=5,visu=T)
Error in cmeans(exprs(eset), centers = centers, method = "cmeans", m =
m,  :
  NA/NaN/Inf in foreign function call (arg 1)
> traceback()
4: .C("cmeans", as.double(x), as.integer(xrows), as.integer(xcols),
       centers = as.double(centers), as.integer(ncenters),
as.double(weights),
       as.double(m), as.integer(dist - 1), as.integer(iter.max),
       as.double(reltol), as.integer(verbose), u = double(xrows *
           ncenters), ermin = double(1), iter = integer(1), PACKAGE =
"e1071")
3: cmeans(exprs(eset), centers = centers, method = "cmeans", m = m,
       ...)
2: mfuzz(eset, centers = c, m = m)
1: cselection(roznSR, m = 1.25, crange = seq(4, 40, 1), repeats = 5,
       visu = T)
> partcoef(roznSR, crange=seq(4,40,1),mrange=seq(1.25,3,0.05))
Error in cmeans(exprs(eset), centers = centers, method = "cmeans", m =
m,  :
  NA/NaN/Inf in foreign function call (arg 1)
> traceback()
4: .C("cmeans", as.double(x), as.integer(xrows), as.integer(xcols),
       centers = as.double(centers), as.integer(ncenters),
as.double(weights),
       as.double(m), as.integer(dist - 1), as.integer(iter.max),
       as.double(reltol), as.integer(verbose), u = double(xrows *
           ncenters), ermin = double(1), iter = integer(1), PACKAGE =
"e1071")
3: cmeans(exprs(eset), centers = centers, method = "cmeans", m = m,
       ...)
2: mfuzz(eset, centers = c, m = m, ...)
1: partcoef(roznSR, crange = seq(4, 40, 1), mrange = seq(1.25, 3,
       0.05))

> sessionInfo()
R version 2.11.1 (2010-05-31)
i686-pc-linux-gnu

locale:
 [1] LC_CTYPE=pl_PL.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=pl_PL.UTF-8        LC_COLLATE=pl_PL.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=pl_PL.UTF-8
 [7] LC_PAPER=pl_PL.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=pl_PL.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] tcltk     stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] Mfuzz_2.6.0        DynDoc_1.26.0      widgetTools_1.26.0
e1071_1.5-25
[5] class_7.3-2        Biobase_2.8.0

loaded via a namespace (and not attached):
[1] tkWidgets_1.26.0


I suppose that it's problem with my imput data, but it's organised in
the
same manner as other datasets, for which no error occured.

I'd checked this data for missing values but there aren't any. It's
looks ok.


Thanks,

Maciej Jończyk, MSc
Department of Plant Molecular Ecophysiology
Institute of Plant Experimental Biology
Faculty of Biology, University of Warsaw
02-096 Warszawa, Miecznikowa 1



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