> However, when I cross-checked the RS numbers in the Promothease report with my raw DNA data, none of the numbers matched.
> Any idea how I should interpret that?
If the rs#s didn't match, promethease wouldn't have told you about them.
If the genotypes for a particular rs# didn't match, you were perhaps seeing snps from the minus strand, which were being affected byhttp://snpedia.com/index.php/Orientation
Can you provide a specific example to clarify what didn't match?