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In the MA plot section "MA and Volcano plots" the description reads:

Each gene is represented with a dot. Genes with an adjusted p value below a certain threshold are shown in cyan (True)

However the code for adding color is using pvalue instead of padj and uses a harcoded value of 0.05:

https://git.mpi-cbg.de/bioinfo/ngs_tools/blob/master/dge_workflow/featcounts_deseq_mf.R#L576

deResults %>% ggplot(aes(0.5 * log2(mean_norm_count_1 * mean_norm_count_2), log2(mean_norm_count_2 / mean_norm_count_1), color = pvalue < 0.05)) +
    geom_point(alpha = 0.1) +
    geom_hline(yintercept = 0, color = "red") +
    facet_grid(condition_1 ~ condition_2)

Expected behaviour Genes coloured by is_hit which reflects the cut-off used in arguments (qcutoff or pcutoff).