[BioC] hclust for 13000 genes

[David K Pritchard]

Avhena,
     I would recommend that you not use R for this application.  For hierarchical clustering of large numbers of genes + visualization I would recommend you try the free MeV program that can handle 20,000 genes easily. 
David


On Wed, 17 Mar 2010, avehna wrote:

> Hi again,
>
> I'm using a very powerful computer (a Mac Pro) with a huge amount of memory
> and it's also very fast, that's why I wondered why this error came out. I
> think the problem is that I'm using R in 32 bit mode. How could I change it?
>
> Regarding the amount of genes: For each treatment by separate the amount of
> genes is smaller, but since I'm interested in making a heatplot to visualize
> the gene profile across all treatments I'm using the union of all sets. I'm
> very open to new suggestions from you.
>
> Thank you so much for your help,
>
> Avhena
>
> On Wed, Mar 17, 2010 at 6:09 PM, michael watson (IAH-C) <
> michael.watson at bbsrc.ac.uk> wrote:
>
>> The first answers is that you need to make sure you computer has enough
>> memory, and that R can access that memory.  See memory.size() and
>> memory.limit() for answers.
>>
>> The second answer is: are you *sure* you want to cluster 13,777 genes?
>>  That's an awful lot to visualise and interpret.....
>> ________________________________________
>> From: bioconductor-bounces at stat.math.ethz.ch [
>> bioconductor-bounces at stat.math.ethz.ch] On Behalf Of avehna [
>> avhena at gmail.com]
>> Sent: 17 March 2010 21:59
>> To: bioconductor at stat.math.ethz.ch
>> Subject: [BioC] hclust for 13000 genes
>>
>> Hi There:
>>
>> I'm trying to cluster 13777 genes that are differentially expressed across
>> three different treatments but I'm getting the following error:
>>
>> ------------------------------------------------
>> R(32949) malloc: *** mmap(size=1518448640) failed (error code=12)
>> *** error: can't allocate region
>> *** set a breakpoint in malloc_error_break to debug
>> Error: cannot allocate vector of size 1.4 Gb
>> Execution halted
>> -------------------------------------------------
>>
>> I wonder how could I fix it in order to get the clusters and the heatmap
>> with the expression profile. I would appreciate any suggestion from you!.
>>
>> Thank you so much for your help in advance,
>>
>> Avhena
>>
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>>
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>
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