The optical intrinsic signal imaging is an indirect mapping of neuronal activity. The change in light intensity due to neuronal activity are often very small, no more than 0.1-6% of the total intensity of the reflected light in optimal cases, and the noise, which arise from either the biological noise associated with the respiration, circulation and irrelevant physiological activity or the instrumentation noise such as digitization noise, illumination noise, movement artifacts, etc. are usually large. In previous studies, a couple of analysis methods such as Standard Difference, Principal Component Analysis (PCA), Independent Component Analysis (ICA), Truncated Differences were used to suppress these large background noises and extract the small signal of interest from the noisy raw data. The performance of these methods for improving the determination of spatial pattern and time course of the response signal were examined and compared in this paper. The evaluations were employed to both simulated data and experimental optical intrinsic signal imaging data from rat somatosensory cortex during the electrical stimulation at contralateral sciatic nerve.