I am a student that recently started working with transcriptomics data.
I am trying to conduct my first single cell data analysis of an organoid model using mainly Seurat. I tried to conduct a differential expression analysis between different clusters using the
FindMarkers() function but I have some questions.
I would like to understand what test would be best to use if MAST or Wilcoxon Rank Sum. I looked at recently published scRNA-seq analysis and they are both commonly used.
I would also like to ask you how you approach the selection of the top DEGs, namely what are the best p_value_adjust and avg_logFC thresholds to use.
I am really new to the field and I would really appreciate any kind of insight.