Is+there+any+reason+to+scan+nitrocellulose+with+pe+instead+of+agilent?

The answer appears to be yes. The forward scanning perkin elmer slides do exhibit a higher ratio when comparing undiluted lysate with empty cell lysate.

This data is from the 11-3-11 nitrocellulose run.

(undilitued median intensity)/(empty cell lysate median intensity) PE Scan 24942/6967 = 3.58 20112/6082 = 3.31

Agilent Scan 6649/2457 = 2.71 6924/2650 = 2.61