The sounder instrumentation on the GOES satellites multispectrally determines precipitable water (Look here [or here] for details; a graphic is available here). Here are some things to keep in mind when viewing the GOES data on these pages. The points below that are important will be repeated when appropriate in the discussion of the GPS/GOES differences.
A B C D E F G H I J K L M N O P Q Rand the sky is cloudy at A, G, and M, the lat/lon will obviously be a little different than if C, I, and O are cloudy. The precipitable water values are computed using 9 points (ABCGHIMNO), then the algorithm steps over 3 columns and uses the 9 points to the right of row CIO (DEFJKLPQR). Each GOES footprint is used only once to compute precipitable water.
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Click here for more information on GPS precipitable water and things to keep in mind about it.