mcvickerlab · Jaureguy760 · Apr 19, 2026 · Apr 19, 2026 · Apr 19, 2026
diff --git a/docs/source/faq.rst b/docs/source/faq.rst
@@ -117,7 +117,7 @@ calibrated for the overdispersion typical of RNA-seq count data.
 
 The standard threshold is FDR < 0.05. For discovery analyses you may want
 FDR < 0.1. For validation or follow-up experiments, consider FDR < 0.01.
-See :doc:`methods/fdr_correction` for details on the BH procedure used.
+See :doc:`methods/statistical_models` for the BH procedure and the NaN-propagation warning.
 
 **My output has very few significant sites. What's wrong?**
 

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -77,12 +77,8 @@ Documentation
    :maxdepth: 2
    :caption: Statistical Methods
 
-   methods/index
-   methods/counting_algorithm
    methods/mapping_filter
    methods/statistical_models
-   methods/dispersion_estimation
-   methods/fdr_correction
 
 .. toctree::
    :maxdepth: 2

diff --git a/docs/source/methods/counting_algorithm.rst b/docs/source/methods/counting_algorithm.rst
diff --git a/docs/source/methods/dispersion_estimation.rst b/docs/source/methods/dispersion_estimation.rst