In February FTDNA announced that they were switching to the Illumina OMNI test chip for their Family Finder autosomal DNA test. Since then people have been gradually getting their test results from the new chip. At this time I have 122 matches from the old Affimatrix chip and 110 from the Illumina chip. They are not all the same and I will be comparing the results from each chip.
In the past I have advised people to do their first autosomal DNA test at 23andme.com since they had a lower cost and they compared the X chromosome, which FTDNA does not currently do. In addition, males got their Y DNA haplogroup and their mtDNA haplogroup. Females got the mtDNA haplogroup. Since FTDNA had announced that they would compare 23andme results to FTDNA Family Finder results, this seemed to be the most cost-effective testing protocol to follow. The switch by FTDNA should make the comparison of results much easier since 23andme also uses an Illumina test chip.