Yikes, you are correct! Thank you so much. I reran the analysis with the
rows and columns switched and it took no time at all.
Thank you again for your help.
On Tue, Nov 17, 2009 at 12:04 PM, Charles C. Berry <cbe...@tajo.ucsd.edu>wrote:
> On Tue, 17 Nov 2009, akonla wrote:
>
>
>> Hi,
>>
>> I am new to clustering in R and I have a dataset with approximately 17,000
>> rows and 8 columns with each data point a numerical character with three
>> decimal places. I would like to cluster the 8 columns so that I get a
>> dendrogram as an output. So, I am simply creating a distance matrix of my
>> data, using the 'hclust' function, and then plotting the results (see
>> below,
>> my data is contained in the text file).
>>
>> x<-read.table('SEP_IR_1113_3.txt', header=TRUE,sep="\t')
>> x.dist=dist(x)
>>
>
>
> See
>
> ?dist
>
> which explains
>
>
> This function computes and returns the distance matrix computed by
> using the specified distance measure to compute the distances
> between the rows of a data matrix.
>
> You are trying to cluster 17,000 rows.
>
> No wonder it (dist) is taking its time!
>
> Chuck
>
> hc=hclust(x.dist,method="average")
>> plot(hc, hang=-1)
>>
>> Unfortunately, the hclust function, although it produces no error terms,
>> takes a very long time to run (>4 hours) and my computer kills the
>> program
>> before it finishes. I don't think this data set is so large to cause such
>> a
>> long computing time, and I have plenty of memory since I am running this
>> analysis on our university computing cluster.
>>
>> Has anyone run into this problem before and does anyone have any tips on
>> how
>> I can speed up processing? I can provide extra information if necessary
>> regarding my problem.
>>
>> Thank you!
>> --
>> View this message in context:
>> http://old.nabble.com/hclust-too-slow--tp26395774p26395774.html
>> Sent from the R help mailing list archive at Nabble.com.
>>
>> ______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
> Charles C. Berry (858) 534-2098
> Dept of Family/Preventive
> Medicine
> E mailto:cbe...@tajo.ucsd.edu UC San Diego
> http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
>
>
>
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