[BioC] HEATMAP on LARGE DATA

[jon butchar]

On Monday 13 March 2006 21:08, mark salsburg wrote:
> I am having trouble getting the function heatmap() to work on the following
> gene expression
>
> > dim(SAMPLES_log)
>
> [1] 12626    20
>
>
>            sample1 sample2...................sample20
> gen1
> gen2
> gen3
> ....
> gen12626
>
>
>
> I have converted SAMPLES_log to a numeric matrix using:
>
> as.matrix(SAMPLES_log)
>
> when I use the following command:
>
> heatmap(SAMPLES_log)
>
> Error: cannot allocate vector of size 622668 Kb
> In addition: Warning messages:
> 1: Reached total allocation of 1022Mb: see help(memory.size)
> 2: Reached total allocation of 1022Mb: see help(memory.size)
>
>
>
> Is there some library in BioConductor that will allow me to output a
> heatmap. I want to compare the expression of the first 10 samples with the
> last 10 samples.
>
> I have tried running that command in a Linux environment, also with no
> success
>
> thank you,
>
> 	[[alternative HTML version deleted]]

Mark, along with the good stuff Sean Davis mentioned, maybe you could think 
about upgrading your computer hardware in the near future.  You can get 
hardware that supports 64-bit memory addressing and put in 4 GB RAM, all for 
about $3k.  That's relatively little compared to what it costs to run 20 
chips.  fwiw, I've compared a 32-bit system against a 64-bit system (both 
with 4 GB RAM), and can heartily recommend just going straight for a 64-bit 
system (hardware _and_ operating system); just fewer headaches.

The number of chips you run will probably only increase during the next 
several years and, as you've discovered, lack of system resources can make 
you lose quite a lot of valuable time.

Best of luck,

jon butchar