Correcting for multiple hypothesis testing using BH FDR correction

[lina....@gmail.com]

Dear LEfSe team,

I have a question about a recent paper:

Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission, The ISME Journal (2014) 8,

1403­1417

You mention that "[s]ignificant P-values associated with microbial clades and functions identified by LEfSe were corrected for multiple hypothesis testing using the Benjamini and Hochberg false discovery rate correction."

Has this been implemented into the LEfSe software available on bitbucket, or was this analyses performed as a separate step?

Thanks a bunch!
~Lina

[Nicola Segata]

Hi Lina,

 the multiple hypothesis testing correction for LEfSe is done as a separate step.

cheers

Nicola 

[lina....@gmail.com]

Great, thanks for clarifying!
~Lina

[Lina L Faller]

Dear Nicola,

If you have it handy, can you make the code you used to perform BH FDR on LEfSe output available? I would like to apply it to some of my own data.

Thanks a bunch!
~Lina

On Thu, Aug 6, 2015 at 3:23 PM, <lina....@gmail.com> wrote:

Great, thanks for clarifying!
~Lina

[Nicola Segata]

Hi Lina,

 I didn't performed the multiple hypothesis testing correction for that work. If I remember well, Michelle (the first author) did it in R....

thanks

Nicola

[Juan Escobar]

Dear Nicola,

I’m a LEfSe user since long time. My colleagues and I recently submitted a paper with some LEfSe results. One of the reviewers asks us to correct such results for multiple comparisons. I can calculate q-values with R but my question is more fundamental. Do you think it’s necessary to correct for FDR the output of LEfSe? I mean, the algorithm is super strict in choosing biomarkers: first Kruskal-Wallis test to choose features differentially distributed among classes, next pairwise Wilcoxon test applied to the retained features and finally LDA bootstrapping support. FDR control should be performed on each step then. I’m aware of a paper you recently published (Rooks et al. 2014, The ISME Journal) in which you performed Benjamini & Hochberg FDR correction on LEfSe p-values. However, I’m wondering if such correction is necessary altogether.

Your thoughts on this topic are welcomed since as far as I have followed publication of LEfSe results, no one applies FDR.

Thanks,

Juan

[Robert Kwapich]

Yes, it would be nice to know the recommendations. I've noticed that some results are significant with LEfSe but when using STAMP to analyse metagenomic profiles of taxa abundances or microbial functions (from KEGG database) some of the result loose statistical power. STAMP has built-in ability to choose FDR method, where Storey-FDR is the recommended one.

I am becoming more skeptical towards LEfSe. In fact a microbiome analyses require double, or even triple checking before reporting something as significant and assigning any meaning to it.

[Stef]

There has been no reply on this issue for almost 7 months. I am concerned about the same thing. If I use lefse as it is, will I get problems when trying to publish due to the lack of multiple corrections? How do I address a reviewer concerned with this?

Thanks for your help!

Stef