The term raw signal values used in the context of Agilent Two Color data refers to the linear data after thresholding and summarization for the individual channels (cy3 and cy5).
Summarization is performed by computing the geometric mean.
The term Normalized signal value refers to the data after ratio computation, log transformation and Baseline Transformation.
In GeneSpring, the sequence of events involved in the processing of the Agilent two color text data files is: Thresholding → Summarization → dye swap → ratio computation → log transformation → Baseline Transformation.