metagenomeSeq: role for fitLogNormal?
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handibles ▴ 10
@handibles-12652
Last seen 4.2 years ago

fitLogNormal is based on the MetaStats package maintained by the MetagenomeSeq developers. It is not clear what this permutation T-Test provides that is not provided by fitFeatureModel with a equivalent number of iterations. 

Is this simply the test that fitFeatureModel calls to do its job?

metagenomeseq • 606 views
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@joseph-nathaniel-paulson-6442
Last seen 4.5 years ago
United States

MetagenomeSeq has a number of tests implemented and available for users, including Fisher's exact test for presence / absence of a feature (fitPA) and a measure of the discovery odds (based on # reads) (fitDO).

fitFeatureModel does not call fitLogNormal. fitLogNormal is solely a permutation based t-test on the log-transformed data - this is an expansion to the main test provided by metastats (multiple covariates could not be included in metastats).

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