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perishky / meffil

Efficient algorithms for analyzing DNA methylation data.
Artistic License 2.0
55 stars 28 forks source link

27k Support #19

Closed jlevy44 closed 4 years ago

jlevy44 commented 5 years ago

Hi there, does meffil offer support for the 27k array? Ideally, I'm looking to conduct a study that would combine 450k, 850k and 27k info.

Thanks!

perishky commented 5 years ago

No, unfortunately it doesn't. Adding 27K support wouldn't be difficult but would require a bit of work handling slight differences between 27K and 450K control probes and adding a 27K annotation.

jlevy44 commented 5 years ago

Yeah that does seem a bit difficult. I suppose would it be okay to preprocess the 27k data using another package and combine it with the 450?

perishky commented 5 years ago

Probably best to apply the same preprocessing to all samples. Seems like you could use the following function in minfi: Ihttps://rdrr.io/bioc/minfi/man/combineArrays.html

jlevy44 commented 4 years ago

Thanks!