I'm diverting this to the more appropriate mailing list, R-help,
since heatmap() is standard R function.
>>>>> "Johan" == Johan Lindberg <[EMAIL PROTECTED]>
>>>>> on Fri, 02 Jan 2004 10:04:14 +0100 writes:
Johan> I am trying to plot a matrix of m-values in a heatmap
Johan> with "average linkage". The rows are M-values of
Johan> genes and the columns are my slides. I do the
Johan> following and get the following error message:
>> heatmap(Matrix[,],Rowv=as.dendrogram(gclus),Colv=as.dendrogram(sclus),col=rbg)
Johan> Error in match.fun(FUN) : evaluation is
Johan> nested too deeply: infinite recursion? Error:
Johan> evaluation is nested too deeply: infinite recursion?
The problem happens when trying to plot a large dendrogram.
The "dendrogam" class is implemented as an S-level "tree", i.e.,
a nested list and plot.dendrogram() uses recursion for
plotting.
To avoid infinite recursion (which would typically "freeze" your
computer), there's a limit in R (and S),
options(expressions = 500)
for how deeply recursions are allowed
to go. The limit is currently too low for the typical
dendrograms that people consider in microarray analysis of
several thousand genes.
Setting
options(expressions = 10000)
should solve the problems for these data sizes.
[when replying to this, please do *drop* [EMAIL PROTECTED] now; it's a n R topic]
Regards,
Martin Maechler <[EMAIL PROTECTED]> http://stat.ethz.ch/~maechler/
Seminar fuer Statistik, ETH-Zentrum LEO C16 Leonhardstr. 27
ETH (Federal Inst. Technology) 8092 Zurich SWITZERLAND
phone: x-41-1-632-3408 fax: ...-1228 <><
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