FoxoTech / methylprep

Python-based preprocessing software for Illumina methylation arrays
MIT License
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Addition of negative control based pvalue calculation #109

Closed notmaurox closed 2 years ago

notmaurox commented 2 years ago

There is utility to a pvalue calculation that only uses negative control intensity when constructing the ECDF. For example - when a chip section is empty (due to operator or automation error), 0% of probes for a sample will pass this pvalue check.

SeSAMe currently supports this functionality: https://github.com/zwdzwd/sesame/blob/master/R/detection.R#L73