from the R side, try increasing the memory limit.
You can check default memory by the command memory.limit()
Alternatively, you can change the memory limit within R using the
memory.limit function, giving a new limit in Mb. (For example, type
memory.limit(2048) to change the memory limit to 2 Gb.)


On Sun, Mar 4, 2012 at 12:05 AM, Salwa Eid <salwaeid@hotmail.com> wrote:

>
>
> limit
>
> Dear all,    Have read dna microarray cel files and normalized the data
> and then tried to use the random forest classifier but i keep getting the
> error "cannot allocate vector of 1.8G".  I had a 3gb ram and upgraded it to
> 8gb and am still getting the same error exactly.  In the first case got a
> warning that it reached total allocation of 3gb and the second case got the
> warning, reached total allocation of 8gb.   The code I used for random
> forest is test<-randomForest(Type~., data=tdata) The tdata is 22215 genes
> for four samples and the type of each sample(2 classes).  Prediction here
> is done for the type.  The tdata is a matrix of 22216 columns which
> consists of 22215 genes and the type and there are 4 rows for four samples.
>  Two types. Any help? Regards,salwa
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>
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