(Importing a new version from external source)
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Indeed, due to Bayer matrix consideration, the RGB result of your RAW image is an interpolated picture. In consequence pre-processing interpolated data will give wrong results. Contrary to RGB image, CFA image represent the entire sensor data with the Bayer pattern. The following image shows you a crop of a CFA image. Note that the Bayer pattern (RGGB on this example) is visible.

Indeed, due to Bayer matrix consideration, the RGB result of your RAW image is an interpolated picture. In consequence pre-processing interpolated data will give wrong results. Contrary to RGB image, CFA image represent the entire sensor data with the Bayer pattern. The following image shows you a crop of a CFA image. Note that the Bayer pattern (RGGB on this example) is visible.