[BioC] Re: [S] Error in clustering procedure

[cstrato]

Sorry, but I cannot resist:

Any comments of the microarry community on the usefulness of
hierarchical clustering of 7000 genes?

Best regards
Christian
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C.h.r.i.s.t.i.a.n. .S.t.r.a.t.o.w.a
V.i.e.n.n.a.         .A.u.s.t.r.i.a
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Prof Brian Ripley wrote:

> A distance matrix on 7000 objects alone takes up 187Mb.  I don't know how 
> your machine is set up re swap space, but you should use your task manager 
> to monitor memory usage.  Almost certainly you are running out of memory.
> 
> However, I have never seen an agglomerative clustering of 7000 objects
> make sense scientifically (not that that stops the bioinformatics people).  
> I think you need either to work in smaller subsets or to combine objects
> into clusters before starting.
> 
> On Tue, 7 Sep 2004, Joao Baptista de O. e Souza Filho wrote:
> 
> 
>>I am working with SPLUS 2000 using Windows 2000 SP4, 512 MBytes RAM,
>>3 GBytes of free space in HD.
>>
>>When I try to do an aglomerative clustering upon a matriz of
>>dimensions 7000 x 5, the program, after some time spent in
>>calculations, returns the following error message:
>>
>>============================================================================================================================
>>Error in disv == -1: Unable to obtain requested dynamic memory (this 
>>request is for 200194252 bytes, 0 bytes already in use)
>>============================================================================================================================
>>
>>First, I have used the command: "options(object.size=300e6)", since the
>>program presented the messsage:
>>
>>=================================================================================================================================
>>Error in double(1 + (n * (n - 1))/2): Cannot allocate 200194208 bytes: 
>>options("object.size") is 100000000: see options help file
>>=================================================================================================================================
>>
>>Does someone know how should I proceed?
>>
>>Thanks in advance
>>
>>Joao Baptista Filho
>>
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> 
>