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Question: Error: cannot allocate vector of size ...
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gravatar for Wall, Dennis Paul
11.9 years ago by
Wall, Dennis Paul80 wrote:
I am trying to run the pam algorithm for k-means clustering, but keep getting the error "Error: cannot allocate vector of size 1048384 K" Any help on how to fix this would be greatly appreciated. Cheers, Dennis
ADD COMMENTlink modified 11.9 years ago by James W. MacDonald46k • written 11.9 years ago by Wall, Dennis Paul80
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gravatar for James W. MacDonald
11.9 years ago by
United States
James W. MacDonald46k wrote:
Wall, Dennis Paul wrote: > I am trying to run the pam algorithm for k-means clustering, but keep > getting the error "Error: cannot allocate vector of size 1048384 K" > > Any help on how to fix this would be greatly appreciated. That error means you are running out of RAM. The quickest, best fix is to get more. Best, Jim > > > Cheers, > > Dennis > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
ADD COMMENTlink written 11.9 years ago by James W. MacDonald46k
Hi Paul, If you've followed that advice or you've already got plenty of RAM you can try the command: memory.limit(2048) This should allow R to use 2Gb of RAM (the max it can use on a normal Windows machine), rather than the 1Gb it defaults too. Mike Smith > Wall, Dennis Paul wrote: > > I am trying to run the pam algorithm for k-means clustering, but keep > > getting the error "Error: cannot allocate vector of size 1048384K" > > > > Any help on how to fix this would be greatly appreciated. > > That error means you are running out of RAM. The quickest, best fix is > to get more. > > Best, > > Jim > > > > > > > > Cheers, > > > > Dennis > > > > _______________________________________________ -- Computational Biology Group Hutchison / MRC Research Centre Department of Oncology University of Cambridge Hills Rd, Cambridge CB2 2XZ Email: mls40 at cam.ac.uk
ADD REPLYlink written 11.9 years ago by mls40@cam.ac.uk30
I'm not sure if this will help, but this is an exerpt from the affy vignette: 5. Read in the data and create an expression, using RMA for example. R> Data <- ReadAffy() ##read data in working directory R> eset <- rma(Data) Depending on the size of your dataset and on the memory available to your system, you might experience errors like 'Cannot allocate vector . . . '. An obvious option is to increase the memory available to your R process (by adding memory and/or closing external applications2 . An another option is to use the function justRMA. R> eset <- justRMA() This reads the data and performs the 'RMA' way to preprocess them at the C level. One does not need to call ReadAffy, probe level data is never stored in an A?yBatch. rma continues to be the recommended function for computing RMA.
ADD REPLYlink written 11.9 years ago by Levi Waldron30
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