On Mon, 19 Oct 2009, Jun Chen wrote:
Dear,
I would like to deal with microarray data, it can run when i deal with
little data. However, the amount number of SNP data are 45181, amount
numbers of animal are 3081,it can not be allocated 1000Mb memory when
i importing them to R
Procedure sentence show:
m<-matrix(scan("D:/SNPdata.txt"),ncol=nmarkers,byrow=TRUE)
Error show:
Error: cannot allocate vector of size 1000.0 Mb
It says you don't have enough memory. When stored as floating point numbers
the SNPs will take up 1Gb, which is quite a lot -- more than you can
conveniently analyze in a 32-bit version of R[*] -- you probably have more than
1Gb of memory, but R does need to make copies of things.
In my experience with SNP data, there are two strategies: storing the data
more efficiently (1 byte/SNP), as the Bioconductor package snpMatrix does, or
reading in just part of the data at a time (what I have usually done). My
approach is to read the data in chunks and store it in a netCDF file with the
ncdf package, and then at analysis time to read data as needed from netCDF.
This also works well for parallel processing -- many R sessions can read
efficiently from the netCDF file.
[*] you didn't provide the requested information about your system, but "D:"
looks Windows.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
tlum...@u.washington.edu University of Washington, Seattle
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