[BioC] R help with large matrices

[Sean Davis]

On Wed, Apr 9, 2008 at 6:31 AM, Ian Roberts <ir210 at cam.ac.uk> wrote:
> Dear All,
>
>  I'm having memory problems producing large matrices and wonder if there is a
>  better way to do what I need?  I'm a novice R user, so here's what I've done
>
>  I need to permute a scoring matrix up to 19,300 events.
>  That is, I have a vector of length 19,300 results and need to compare each with
>  each other for all possible permutations therein of the type N!/(N-n)!

Unless you have a pretty big machine, you will probably not be able to
fit a 19,300 x 19,300 member matrix into memory.  Why not use a random
sampling of a set size (say, 1000 events)?  Sample() is the function
that chooses random samples.

That said, you may want to describe what you are trying to do, rather
than asking how to do it.  There may be a bioconductor package that
already answers the question you are trying to answer.  In particular,
there are numerous CGH array packages.

Sean

>  I've tried writing my own, and the permutations function of package gtools,
>  however both run into trouble with vectors in excess of 1000 events.
>
>  Essentially, the score matrix provides start and stop clone numbers for an
>  ordered gene list.  It works well for BAC arrays, but is failing for Agilent
>  244K oligo arrays!!!