[BioC] Removing probes before or after normalization

[Bornman, Daniel M]

Dear BioC,

I have a cutom chip with multiple microbial organisms but I am currently
only interested in the results for one of these.  At what step in the
analysis process is it adviced to remove the other organisms from
analysis.  I worry that probes specific to those 'other' organisms may
contribute to the background noise.  In that case maybe I should remove
them prior to normalization and background correction.  Otherwise, maybe
prior to independent testing and p-value adjustment. And, if not there,
then prior to annotation.


Thank You,

Daniel Bornman
Researcher
Battelle Memorial Institute
505 King Ave
Columbus, OH 43201
614.424.3229