[BioC] sigPathway on Agilent data

[Srinivas Iyyer]

Dear group, 
How can I do sigPathway analysis for an agilent
experiment. 

My experimental design:
I have 10 chips data. 

Chips are hybridized by normal and treated from same
mouse. 

sigpathway requires a phenotype label file:
indicating 0 (say normal) and 1 (disease). 

In case of my experiment (two color, matched sampleS)
how can I define phenotype file.

Any suggestion who have worked out Agilent dual
channel data for this kind of design.

thank you in advance. 

srini