[BioC] Tiling array application

[Shinhan Shiu]

We are trying to use GCRMA to adjust raw intensity values from tiling chip 
experiments (Arabidopsis). But the affy Arabidopsis tiling chip do not have 
mismatch probes and it seems the mismatch probe intensity is absolutely 
required in:

bg.parameters.ns

Where the mismatch probe intensities, mismatch probe affinity, and perfect 
match probe affinities are passed. I wonder how this function can be 
modified so only perfect match probe info is used. Thanks.

Shinhan


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  Shinhan Shiu
  Dept. of Ecology and Evolution
  University of Chicago