How to analyse 450k and EPIC methylation data together?
1
0
Entering edit mode
maduran • 0
@maduran-21749
Last seen 2.1 years ago

I have 450k and EPIC data that I would like to process at the same time and analyse the whole matrix at once. I am using minfi package, which contains the combineArray() function that is intended to merge 450k and EPIC data. However, when using it, it automatically drops all the probes in the EPIC array that are not in the 450k array, which is totally an unwanted behaviour since I lose half of the probes of the EPIC array. Does anybody know an alternative solution to analyze both platforms together?

minfi version 1.30.0

Many thanks in advance,

minfi 450k EPIC analysis • 410 views
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 1 day ago
United States

If you don't drop the EPIC-only probes, your matrix will have this great huge block of probes that are NA for all the samples that were run on the 450K arrays, for which any analysis will only use the EPIC data. So it doesn't make any sense to do anything but drop the EPIC-only probes, because you can just analyze those separately anyway.

ADD COMMENT

Login before adding your answer.

Traffic: 167 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6