The two tests are not really comparable.
I was not familiar with GI MAP so read up about it. It is almost entirely DNA based, with a couple of useful gut markers thrown in. It concentrates on gut pathogenic species (bacteria, fungi, parasites and a couple of viruses) plus throws in a couple of less problematic bacterial inhabitants.
The GI Effects test is essentially an old fashioned CDSA test with a little bit of DNA -based analysis grafted on to make it appear to be an up-to-date test.
There are a few useful markers reported in a CDSA, such as SCFA's (which aren't reported in GI MAP), but I think the culture-based analysis and the parasitology are largely a waste of time. The former technique selects for aerotolerant organisms which are easy to culture, but these are a small minority of the gut inhabitants; the picture given of supposed overgrowths is completely distorted.
See
this post.
Furthermore, many parasites are fragile and are not preserved by the CSDA collection technique.
The selection of genera/species chosen for the DNA based analysis is also a bit puzzling - there doesn't seem to be much reason for choosing those particulars ones.
So the GI-MAP test is more sensitive and reliable for the species that it tests for and seems like a good test to have if you suspect that you have some kind of gut pathogen. It does not, however, give a comprehensive picture of what is going on in your gut.
DNA-based tests like those offered by uBiome.com (the explorer test) do attempt to sequence all bacteria and archaea in the gut so give a comprehensive picture, though understanding what the results mean is something that needs work. See
this post and
this thread.
uBiome has recently started offering a Smart-Gut test which focusses on specific gut bacteria for which there is good background knowledge. It is worth some consideration also.