Hi, I'm quite new in Microarray analysis so my question is very basic. I'm working with an Affymetrix Genome-Wide Human Origins Array 1. After the Genotyping, I've worked on the tped file in order to remove several positions. My question is related to those Probes with missing rs code. They are labelled either " --- " or " " (empty column).
Can I remove them? Is there an optimal percentage of removal? If I remove them, I would have a 5.89% of positions removed. What do you think?