Answers.Body: <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>
  
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Answers.Text: yes fig5D ."In the methods they describe that they use Fluidigm (i.e. RT-qPCR) for gene expression, not RNA-seq." okay i think i have to read it ,i missed it .
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Body: <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>
  
Tags: <rna-seq><figure-reproduction>
Title: log2fold change as heatmap
ThreadText: # log2fold change as heatmap
  
  (Asked by: username_0 on 2019-04-08)
  
  From a [paper](https://www.ncbi.nlm.nih.gov/pubmed/29628141):
  
  > (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](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE101004) where I see three wild type and three knockout.
  
  **Tags:** rna-seq, figure-reproduction
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2019-04-08. Score: 1 | Accepted answer
  
  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.
  
  > **Comments:**
  > **username_0**: yes fig5D ."In the methods they describe that they use Fluidigm (i.e. RT-qPCR) for gene expression, not RNA-seq." okay i think i have to read it ,i missed it .  
  
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