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

Wang, Hui Hui_Wang at affymetrix.com
Sun Mar 16 10:41:59 MET 2003

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 at exprs #where test.intensity is a 0.5 miliion x 5


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





-----Original Message-----
From: Wang, Hui 
Sent: Saturday, March 15, 2003 1:35 PM
To: bioconductor at stat.math.ethz.ch
Subject: pm or mm methods for AffyBatch object


Hi List,


I have two questions:


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?



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



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