LogR and LogOR, log2 or natural log

mskcc / facets

Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.

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Open cytrix1 opened 5 years ago

cytrix1 commented 5 years ago

In FACETS, log2 is used in LogR and natural log is used in LogOR? Is it correct?

I am wondering how P(g) term in likelihood is determined. Is it evenly distributed and updated during iteration?

Thank you very much!

Young

veseshan commented 5 years ago

For log-ratio fold change makes sense and so log2 is easier to interpret. For odds-ratio natural log is easier for distributional properties.