DNA differential methylation analysis for Illumina Human Methylation 450k and 27K arrays

Question

[fatemehseyednasrollah]

I am planning to run differential methylation analysis for a dataset of which some samples are sequenced using Illumina Human Methylation 450K array and some 27K array. Is it safe to combine the samples from different platforms based on common probes (obviously mostly covering 27K and loosing all 450K additional probes) and run the differential methylation analysis? Thanks for the help.

[Mattias Aine]

Possibly, the platform is fairly robust but always do a sanity check on the results.

A potential problem could of course be if 'group1' has been run on 27K and 'group2' on 450. Then you cant really say the results are due to a true g1-g2 difference. Although I could still believe the results if you apply a reasonable minimum delta-beta cutoff..

Answer 1

[sviatoslav.kendall]

I think you should be OK doing that but pay attention to which reference genome you're using. I think the 27K probes might be based on an older build than the 450K.