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HasanThePupil 03-31-2018 12:54 PM

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.

thermophile 04-02-2018 08:28 AM

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.

asorbie 04-04-2018 02:48 AM

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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