Dear list, It turned out the slowness and out of memory has nothing to do with bioconductor package. I tested it by the following: test.intensity <- test@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. Best regards -h -----Original Message----- From: Wang, Hui Sent: Saturday, March 15, 2003 1:35 PM To: bioconductor@stat.math.ethz.ch Subject: pm or mm methods for AffyBatch object Hi List, I have two questions: 1) I have a chip which is the same feature as u133A, however have much less mm probes. When using pm or mm method, the matrices have the same dimension. I wonder, do the methods assume the number of probes for pm or mm are the sames by default? How do you determine pm or mm probes? 2) The cdf I am using is the same size as u133A(I wish I could contribute my cdf), I only read in 5 chips. However running into memory problem quickly. For example, I did a boxplot on 5 chips, it gave memory error (I allocated 1G) after 10mins of plotting. Could somebody give me some tips besides breaking down the files (since I only have 5 files)? Best regards -h [[alternate HTML version deleted]]

Hi, > > test.intensity <- test@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