[R] out of colors in Mclust with 12 clusters

From: Mark W Kimpel <mwkimpel_at_gmail.com>
Date: Wed, 26 Mar 2008 02:38:59 -0400


I'm running Mclust 3.0 in R-2.7.0 and have run into a situation where the optimal number of clusters, 12, seems to be greater than the number of colors available to Mclust. The code below, which demonstrates errors, does not if the max no of clusters is set at 10. sessionInfo, after a restart of R and loading of packages, follows the output.

Is this a known problem with Mclust? Can I supply more colors?

As an aside, Mclust is crashing when it runs out of memory with high dimensional datasets. R and Emacs freeze, my SystemMonitor in Ubuntu shows that the CPU grinds to a halt but the memory is exhausted. Shouldn't a process in R exit and return an error when memory can no longer be allocated? Wishful thinking????

Mark

> exprs.clust <- Mclust(exprs(AOP.sig), G=9:12, modelNames="VEI")
Warning messages:
1: In summary.mclustBIC(Bic, data, G = G, modelNames = modelNames) :

   best model occurs at the min or max # of components considered 2: In Mclust(exprs(AOP.sig), G = 9:12, modelNames = "VEI") :

   optimal number of clusters occurs at max choice
> plot(exprs.clust, data = exprs(AOP.sig))

Hit <Return> to see next plot:
Hit <Return> to see next plot:
Hit <Return> to see next plot:
Hit <Return> to see next plot:

Warning message:
In clPairs(data[, 1:min(5, p)], classification = x$classification, :

   more colors needed
> myMclustOutput.func(exprs.clust)

#Above just outputs the classificatin and uncertainty in a data.frame. #Usually works fine
Error: bad value
No suitable frames for recover()
> 2 + 4

Error: bad value
No suitable frames for recover()
> sessionInfo()

Error: bad value
No suitable frames for recover()

#After R-devel restart

> sessionInfo()

R version 2.7.0 Under development (unstable) (2008-03-05 r44683) x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:

[1] lme4_0.99875-9       Matrix_0.999375-5    lattice_0.17-6
[4] affy_1.17.9          preprocessCore_1.1.5 affyio_1.7.17
[7] Biobase_1.99.3       mclust_3.1-3

loaded via a namespace (and not attached): [1] grid_2.7.0
>

-- 

Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN  46074

(317) 490-5129 Work, & Mobile & VoiceMail
(317) 204-4202 Home (no voice mail please)

mwkimpel<at>gmail<dot>com

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Received on Wed 26 Mar 2008 - 09:33:55 GMT

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