FindMarkers DESeq2 p-values

[Yanst86]

Hi all,

I have two questions about the p-values shown for FindMarkers using DESeq2 method on AggregateExpression data (following similar steps as described in the 'Perform DE analysis after pseudobulking' in the 'Differential expression testing' vignette):

1. Does the 'p-val' column still calculate non adjusted p-value and the 'p_val_adj' column calculates adjusted p-value using Bonferroni correction?
2. In bulk RNA-seq, the usual correction method is FDR/Benjamini Hochberg (BH) while Bonferroni is considered to be too stringent in most of these analyses. Using the same logic, does it make sense to correct the p-value shown in 'p-val' (assuming this is the non-adjusted p-value) by using FDR/BH following 'FindMarkers' analysis using DESeq2 method?