I am inspecting DNAm data in GEO, and I have come across one peculiar detail and I don't know what to make of it.
Shortly, various samples marked as female contain non-zero values for Y-chromosome specific CpG sites. Let me illustrate:
- Here is an entry for a female sample (GSM1401202)
- Let's check CpG site cg03515901. In the platform data table, column 9, line 3657 we find that this CpG is located on Y chromosome;
- And now let's see what the female sample has at this site LINK
That could be a one-off mistake, but from what I've seen that happens quite frequently in female data. Has anyone encountered this issue? Why? How? What do?