[BioC] pm or mm methods for AffyBatch object

[Wang, Hui]

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


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