[BioC] RE: pm or mm methods for AffyBatch object

Wolfgang Huber whuber at jimmy.harvard.edu
Sun Mar 16 15:58:40 MET 2003


> 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), ])


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