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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 Jo?czyk, 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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Hi! I've tried but can't do it solve this problem. I have a matrix with genes (col = 1) and expression values (col = 2, 3 and 4). I try to use the soft clustering library Mfuzz, but an error in cmeans don't let me plot the clusters. Anyone to give me a hand, please?
Thanks!