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  • Simple statistics help

    Hello there,

    I am currently working on a metagenomics project on the oral microbiome. I am new to metagenomics and not the best at statistics, so please bear with me

    I have 3 conditions: a control, an antibiotic-treated, and another type of antibiotic-treated.

    I was referred to Metaphlan2, which turned out to be great. Super grateful for the tool. Generated a nice heat map and got some nice preliminary results.

    However, I am interested in only extracting bacterial species that have a differential relative abundance of some threshold across treatment groups. What is the easiest way to do this given the output metaphlan2 output (relative abundance)? Any help would be appreciated.

  • #2
    I start with indicator species analysis (indicspecies package in R). you'll need to correct the p-values for multiple comparisons, the package doesn't automatically do that.
    Microbial ecologist, running a sequencing core. I have lots of strong opinions on how to survey communities, pretty sure some are even correct.

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    • #3
      From the same guys that created Metaphlan there's also a tool called LEfSe which you could use for this. It may be easier for you if you're new to this!

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