Why might Affymetrix GeneChip Mapping assays interfere with the REPLI-g FFPE kit?
FAQ ID -1755

Affymetrix GeneChip Mapping assays require restriction sites for the digestion with enzymes. Due to the procedure of random DNA ligation when using the REPLI-g FFPE Kit, original restriction sites may be lost. Therefore, we do not recommend this kit in combination with the Affymetrix GeneChip procedure.

Affymetrix Targeted Genotyping assays on the other hand use a primer extension protocol and should be compatible with the REPLI-g FFPE procedure as they are not affected by the random ligation process.