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FrederickHuangLin / ANCOMBC

Differential abundance (DA) and correlation analyses for microbial absolute abundance data
https://www.nature.com/articles/s41467-020-17041-7
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Log fold change #11

Closed ntromas closed 3 years ago

ntromas commented 3 years ago

Hi,

Very naive question: I wonder if negative log-Fold change are conserved in ANCOMBC output.

Cheers,

FrederickHuangLin commented 3 years ago

Hi @ntromas,

Thanks for your question!

Yes, ANCOMBC will output negative log-fold changes. Section 3.4.1 of this vignette shows an example of betavalue output and it contains both positive and negative values.

Best, Frederick

benyoung93 commented 3 years ago

Good afternoon Apologies for this probably simple question, but the beta output gives negative and positive LFC. Is this therefore a log-fold change, or a log-2-fold change.

This is always one of those things I look up, learn, and forget but just wanted to double check to make sure I am using correct terminology in writing of my results. If I am correct in my thinking, it must be a log2 fold change as it has negative values (which with only the log would be 0-1).

Thank you for the help and apologies for the simple query. Benjamin

FrederickHuangLin commented 3 years ago

Yes, it is log-fold change but in natural base, i.e., log(e)-fold change.

Huang