log = TRUE option for get_normalized returns the natural log?

[cypranowska]

I usually log2 transform (with a pseudocount) my normalized expression data before doing further work, and was surprised to find that the log = TRUE option for get_normalized returns the log1p transformed matrix.

Would it be possible to make a log2(x+1) option for get_normalized? Or explicitly mention that the natural log is returned in the documentation?

[mbcole]

Hi @cypranowska - thank you for your feedback! I think we can ultimately address this space with user-provided log-transformations and inverses. This would become an additional argument for modifying the adjustment step, stored internally for future use. In the meantime we can improve our documentation of the log-transformation / inverse (log1p,exp1m) being used in this package.

[cypranowska]

Thank you!