From a paper:
(D) Expression analysis of multiple lineage-specific differentiation markers in WT and PUS7-KO EBs (14 days). Heatmap shows log2 fold change (FC) PUS7-KO to WT for each individual gene (rows) in three independent experiments (columns).
They have analysed the data in EdgeR but I was wondering how did they plot fold change when they have two condition but they have three independent experiment, I haven't used EdgeR so far, use DESeq2 where I group my biological replicate. For example if I have two condition with three biological replicate then I would group them and analyse, in case of DESeq2 I would get final result with one fold change report.
How did they do in this case reporting three fold change ?
Data sets where I see three wild type and three knockout.