[BioC] pm or mm methods for AffyBatch object

Wolfgang Huber whuber at jimmy.harvard.edu
Sun Mar 16 11:45:44 MET 2003

On Sat, 15 Mar 2003, Wang, Hui wrote:
> 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?

Hi Hui,

it depends on the CDF file (or CDF package) that you are using. If that
says that there's are a one-to-one relationship between PMs and MMs, then
the package will also behave so. It is fairly easy to calculate expression
values ignoring the MM values. If you want to do more complex setups with
varying arrangements of PMs and MMs (if that distinction is still
meaningful...?) , you probably will want to dig into the code - have a
start at the function express(), and have a look at the structure of the
CDF environments.

Best regards

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