User: handibles

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handibles10
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Posts by handibles

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Comment: C: DESeq2 Differential Abundance with non-OTU data (e.g. PICRUSt)
...    Thanks for the response, sorry for not being clearer. I would like to use DESeq2 to test for differential abundances in predicted gene content between samples, much as testing for differential 16S abundance. My concern is that methods like PICRUSt mutate (i.e. 16S-copy normalisation, gene inferen ...
written 2.5 years ago by handibles10
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DESeq2 Differential Abundance with non-OTU data (e.g. PICRUSt)
... Hey all,    I'm analysing a 16S microbial community dataset, and am using DESeq2 to test for differential abundances. When I do this, I supply raw count information to DESeq() as per the vignette rationale that the model fitting implicitly assumes raw count data. If I want to later try e.g. ordinat ...
deseq2 picrust written 2.5 years ago by handibles10
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Comment: C: Difference between fitFeatureModel and fitZIG in metagenomeSeq
... Apologies, I'll try to correct & clarify: By 'multiple testing' I meant fitFeatureModel doesn't seem to allow for comparisons between groups (e.g. A v. B v. C v. D. etc), while fitZig does (section 4.2) - if attempted it simply gives the exception 'Can't analyse currently' (apologies if I've ...
written 2.6 years ago by handibles10
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metagenomeSeq: role for fitLogNormal?
... 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 written 2.6 years ago by handibles10 • updated 2.6 years ago by Joseph Nathaniel Paulson270
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Answer: A: Difference between fitFeatureModel and fitZIG in metagenomeSeq
... I'd like to second Sasha's request for clarifications on the ZIG and Feature Model methods, and the recommended use of these tests. From the metagenomeseq.pdf page 16: " This is our latest development and we recommend fitFeatureModel over fitZig [...] By reparametrizing our zero-inflation model, we ...
written 2.6 years ago by handibles10
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metagenomeSeq 1.16.0: unique features give NA's for logFC / p-val?
... Hey Devs,    Thanks for the package and it's upkeep. I've hit a snag comparing two conditions (A=6 samples, B=9 samples), wherein feature counts in A = 0 or 1, counts in B =100 - 15,000, but the logFC and p-values are NA/NaN's. +samples typically are all of one group, 1-0 of the other.    I would ...
metagenomeseq written 2.6 years ago by handibles10 • updated 2.6 years ago by Joseph Nathaniel Paulson270

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