Why does minfi impute actual values in place of NULL values when normalizing methylation data?

Question

[sbdejene]

Hello,

I have a methylation file with raw beta values that I am trying to normalize. There are some probes excluded from the data due to not passing QC, and those excluded probes have been denoted as "NA".

When I normalize the beta values with minfi, it gives normalized beta values even for those cpgs that were denoted as "NA" for a particular sample.

It shouldn't be possible for an "NA" value to be normalized to an actual value, unless there is something I am missing? Is it inputting a default value? And if so, how is that determined?

Answer 1

[sbdejene]

Unfortunately there's no way to delete your own question, otherwise I would!

I was checking the beta values normalized from the IDAT files with the raw beta values that I had received from the core that ran the assay for us. I have no actual evidence that the beta values extracted from preprocessRaw had missing values, I will definitely check --but there shouldn't be. This issue is resolved.