Author: Sofia Morfopoulou; Vincent Plagnol
Title: Bayesian mixture analysis for metagenomic community profiling. Document date: 2014_7_25
ID: 058r9486_11
Snippet: The user's choice for this key parameter r should be informed by the biological context. As an example, for the typical human clinical sample where the sample collection might have occurred some time after the infection has taken place, a low value in order to adopt a sensitive approach is reasonable. Hence, for viral identification in human clinical samples, a low and sensitive value (r = 10) is a reasonable choice. In a highly complex environme.....
Document: The user's choice for this key parameter r should be informed by the biological context. As an example, for the typical human clinical sample where the sample collection might have occurred some time after the infection has taken place, a low value in order to adopt a sensitive approach is reasonable. Hence, for viral identification in human clinical samples, a low and sensitive value (r = 10) is a reasonable choice. In a highly complex environmental metagenomic community where there is a plethora of species of similar abundances, the choice becomes less straightforward especially in the case of closely related strains. We set the default value for general community profiling in environmental samples to be r = 30. We also compare the output of metaMix for different values of this parameter. Supplementary Text 1 presents a detailed discussion on these settings as well as practical considerations.
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