[BioC] RE: pm or mm methods for AffyBatch object
Wolfgang Huber
whuber at jimmy.harvard.edu
Sun Mar 16 15:58:40 MET 2003
Hi,
>
> test.intensity <- test at exprs #where test.intensity is a 0.5 miliion x 5
> matrix
> plot(data.frame(test.intenisty)) # scatter plot for replicate comparison.
> it took >10 mins after I increased the memory size. (I was running the
> window version of R). As you can see that have nothing to do with
> biocondunctor package.
Plotting a scatter plot with half a million points will certainly take
forever; if you tried to save the plot or copy/paste it across to other
applications, you would also see that it becomes huge! And finally, you
will need see very much except for a big black mess. Consider:
- using the hexbin package
- subsampling, i.e.
plot(test.intensity[sample(nrow(intensity), 1e4), ])
Cheers
Wolfgang
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