text: user285: 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.
  
  user939: If I read quickly thru the paper, I see you refer to Fig 5D. In the methods they describe that they use Fluidigm (i.e. RT-qPCR) for gene expression, not RNA-seq. The data link you give is for small-RNA-seq.
  
original_text: 285: <p>From a <a href="https://www.ncbi.nlm.nih.gov/pubmed/29628141" rel="nofollow noreferrer">paper</a>:</p>
  
  <blockquote>
    <p>(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).</p>
  </blockquote>
  
  <p>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.</p>
  
  <p>How did they do in this case reporting three fold change ?</p>
  
  <p><a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE101004" rel="nofollow noreferrer">Data sets</a> where I see three wild type and three knockout.</p>
   939: <p>If I read quickly thru the paper, I see you refer to Fig 5D. In the methods they describe that they use Fluidigm (i.e. RT-qPCR) for gene expression, not RNA-seq. The data link you give is for small-RNA-seq.</p>
  