Qvalue fdr microbiota normal

The Benjamini–Hochberg method was used to control the false discovery rate (FDR), with a Q value (FDR P) < being considered statistically.

They examine taxa individually and use the q value method [19] or the Benjamini-Hochberg (BH) procedure [20] to control the false discovery rate.

We considered an FDR-adjusted p value (q value) less than as significant.

P-values were FDR-adjusted using the p-value distribution (Storey et al., ) and q-values are indicated in the results.

However, if you want to restrict your results to only biomarkers you have confidence in then a lower cut-off of or is typical.

We considered an FDR-adjusted p value (q value) less than as significant.!

Understanding p value, multiple comparisons, FDR and q value

UPDATE 01/29/2019. Read this awesome paper Statistical tests, P values, confidence intervals, and power: a guide to misinterpretations.

This was an old post I wrote 3 years ago after I took HarvardX: PH525.3x Advanced Statistics for the Life Sciences on edx taught by Rafael Irizarry.

It is still one of the best courses to get you started using R for genomics. I am very thankful to have those high quality classes available to me when I started to learn.

Endogenous signaling levels measured by CyTOF and identified as significantly changed (FDR ≤ , q-value ≤ , SAM test using siggenes.

I am reposting it here using blogdown to give myself a refresh.

I am writing this post for my own later references. Deep understanding of p-value, FDR and q-value is not trivial, and many biologists are misusing and/or misinterpreting them.

Please also read this Nature Biotech primer How does multiple testing correction work?

For biologists’ sake, I will use an example of gene expression. Suppose we have two groups of cells: control and treatment (can be anything like ch