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joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
http://joey711.github.io/phyloseq/
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ALDEx2 package? #701

Closed ianpgm closed 7 years ago

ianpgm commented 7 years ago

Hi Joey, just a quick question - you recommend DESeq2 for differential abundance analysis when using phyloseq. I was wondering if you had considered the ALDEx2 R package, and if you had chosen not to recommend it if there was a specific reason why? I recently read Fernandes et al. 2014 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4030730/), and that talks about the ALDEx2 package solving the same problem that DESeq and edgeR do, although in a very different way. The advantages and disadvantages of the different methods used in these different packages are still over my head, so I was wondering if you or Susan had some insights?

spholmes commented 7 years ago

Hi, The problem with that approach is that the authors make the data into compositional data which they are not and the consequences are that if the overall level of bacterial abundances drops (for instance when taking antibiotics) then the method is invalid. We recommend DESeq2 and edgeR because there are thousands of RNASeq papers that have already validated the models and statistics. The only caveat is that if there really are too many zeros, one should do a zero inflated model first, this has actually been done by several authors. Susan

On Tue, Jan 10, 2017 at 7:16 AM, Ian Marshall notifications@github.com wrote:

Hi Joey, just a quick question - you recommend DESeq2 for differential abundance analysis when using phyloseq. I was wondering if you had considered the ALDEx2 R package, and if you had chosen not to recommend it if there was a specific reason why? I recently read Fernandes et al. 2014 ( http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4030730/), and that talks about the ALDEx2 package solving the same problem that DESeq and edgeR do, although in a very different way. The advantages and disadvantages of the different methods used in these different packages are still over my head, so I was wondering if you or Susan had some insights?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/joey711/phyloseq/issues/701, or mute the thread https://github.com/notifications/unsubscribe-auth/ABJcvZJb_zrPPznBVXoys_ZKba4Q49oaks5rQ6DEgaJpZM4Lfhn5 .

-- Susan Holmes Professor, Statistics and BioX John Henry Samter Fellow in Undergraduate Education Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/

ianpgm commented 7 years ago

Thanks Susan, that answers my question!