How to do LEfSe test and get p-value and std deviation values on the data obtained from Qiime2?

[danielsebas (Daniel)]

Dear Friends,

I have 4 sets of sequenced data of water samples. Each sample set has 10 samples. Can you please let me know how can I perform p-value and std deviation analysis from the data generated by QIIME analysis. I have performed all analysis from QIIME like, taxa composition, beta diversity, core-metrics to get an idea of the diversity and composition of bacterial communities in water samples. the reference paper is this:

Reduced microbiome alpha diversity in young patients with ADHD

Thanks much!

[Nicholas_Bokulich]

Hi @danielsebas,
If you want to perform a differential abundance test, you can use qiime composition ancom (see the tutorials at qiime2.org for examples, e.g., the "moving pictures" or "parkinson's mouse" tutorials both use ANCOM).

There is also a new differential abundance plugin that joined the QIIME 2 family ():

Differential abundance analysis with q2-aldex2

q2-aldex2 More documentation is available in the plugin library. ALDEx2 is a differential abundance package that was initially developed for meta-RNA-Seq, but has performed very well with traditional RNA-Seq, 16S rRNA gene sequencing, and selective growth-type (SELEX) experiments. In principle, ALDEx2 is generalizable and can be applied to nearly any type of data that is generated by high-throughput sequencing that generates tables of per-feature counts for each sample Fernandes 2014. Here we w…

LEfSe is not part of QIIME 2 — if you want to use LEfSe you should check out the appropriate manual or post to the LEfSe forum to learn more about formatting for that method.

[danielsebas (Daniel)]

Thanks @Nicholas_Bokulich, could you please let me know how can I get p-values for the samples? Thanks!

[Nicholas_Bokulich]

ANCOM does not return individual p-values. You can read a little more by searching the forum archives or reading the original paper about ANCOM.

[danielsebas (Daniel)]

Thanks @Nicholas_Bokulich. I understand ANCOM does not return P-values, I already read about it. I wanted to know if you could suggest how can I get P-values for each sample, so significance across the sample sets can be assessed? thanks.