Hi there,
I'm brand new to R, so let me know if this question is not
appropriate for this list. I've been reading through the
documentation and have tried a number of things, but am pretty much
stuck so far. Here's the session info:
> sessionInfo()
R version 2.6.2 (2008-02-08)
i386-apple-darwin8.10.1
locale:
C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] rcompgen_0.1-17
So I seem to be hitting a limit on matrix size. First I read in my
data into a list and it's OK:
> mz <- scan("data.column3.txt", list(0))
Read 158991 records
>mz
> mz
[[1]]
[1] 0.000000e+00 0.000000e+00 1.003393e+01 3.651888e+00 0.000000e
+00
[6] 0.000000e+00 3.067042e+00 1.277249e+00 1.984366e+00 3.644203e
+01
[11] 1.172925e+02 1.933753e+02 2.020940e+02 1.570501e+02 8.990829e
+01
...
But when I try to put it into a matrix like this, I don't get an
error, but the matrix appears empty...
> MZ=matrix(mz[[1]],nrow=1)
> MZ
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,
9] [,10]
[,11] [,12] [,13] [,14] [,15] [,16] [,
17] [,18]
[,19] [,20] [,21] [,22] [,23] [,24] [,
25] [,26]
...
When I did a subset of my data, it was fine. I did a manual binary
search and determined the cutoff to be 100000 elements. So if I do
just 99,999 elements, it looks as I would expect:
> mz <- scan("data.column3.txt", list(0), 99999)
Read 99999 records
> tst <- matrix(mz[[1]],nrow=1)
> tst
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,
9] [,10]
[1,] 0 0 10.03393 3.651888 0 0 3.067042 1.277249 1.984366
36.44203
[,11] [,12] [,13] [,14] [,15] [,16] [,
17] [,18]
[1,] 117.2925 193.3753 202.0940 157.0501 89.9083 26.44127 17.05373
53.40315
[,19] [,20] [,21] [,22] [,23] [,24] [,
25] [,26]
[1,] 65.20086 37.33463 17.71247 27.37268 41.83289 48.46916 58.94969
76.05099
...
If I do 100,000, I get the same empty appearance. I've assumed that
there must be a limitation on the number of elements in a matrix. Is
that right? If so, how do I increase the maximum number of
elements? I tried another machine's installation of R and it
apparently doesn't have a 99,999 element limit. I've tried using:
R --max-mem-size=2G
R --max-vsize=200000
R --max-nsize=200000
R --max-vsize=200000 --max-nsize=200000 --max-ppsize=200000
R --max-vsize=10M
I still end up with the empty-looking matrix when I try these. How
do I get my installation to work like the installation on another
computer I tried where I was able to have larger matrices?
Oh yeah, I also tried this, just to rule out problems with my data:
> tst <- matrix(seq(1,158991),nrow=1,ncol=158991)
> tst
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
[,13] [,14]
[,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,
25] [,26]
[,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,
37] [,38]
...
Thanks,
Rob
Robert W. Leach
Scientific Programmer
Center for Computational Research
Center of Excellence in Bioinformatics
University at Buffalo
http://www.ccr.buffalo.edu/
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