On 03/04/2012 07:49 AM, Alpesh Querer wrote: > 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.) It's useful to remember that this kind of error message often means "I've already allocated a lot of memory, and cannot allocate an additional 1.8G". It is often useful to filter the input to machine learning algorithms, e.g., selecting a subset of the most variable (and hence most statistically informative, by a robust measure of variability) genes. See the genefilter package. Martin > > > On Sun, Mar 4, 2012 at 12:05 AM, Salwa Eid<salwaeid at="" 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 >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793