Simple statistics help

HasanThePupil · 03-31-2018, 12:54 PM

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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03-31-2018, 12:54 PM	#1
HasanThePupil Junior Member Location: Virginia Join Date: Mar 2018 Posts: 1	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.

04-02-2018, 08:28 AM	#2
thermophile Senior Member Location: CT Join Date: Apr 2015 Posts: 243	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.

04-04-2018, 02:48 AM	#3
asorbie Junior Member Location: Munich Join Date: Jun 2017 Posts: 8	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!