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

[Maciej Jończyk]

Dear List Members,

I've found response on my question.

http://article.gmane.org/gmane.science.biology.informatics.conductor/33034/match=na+nan+inf+foreign+function+call
It was problem with rows with 0 variance.

Best,

Maciej Jończyk <mjonczyk at biol.uw.edu.pl> nadawca :

> 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
>
>
>
> ___________________________________
> NOCC, http://nocc.sourceforge.net
>
>
>


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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