Question: How to analyse 450k and EPIC methylation data together?
0
gravatar for maduran
3 months ago by
maduran0
maduran0 wrote:

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 analysis epic • 84 views
ADD COMMENTlink modified 3 months ago by James W. MacDonald52k • written 3 months ago by maduran0
Answer: How to analyse 450k and EPIC methylation data together?
0
gravatar for James W. MacDonald
3 months ago by
United States
James W. MacDonald52k wrote:

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 COMMENTlink written 3 months ago by James W. MacDonald52k
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