<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>

CC BY-SA 4.0
2019-04-08T09:25:20.130Z
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 .
kcm
CC BY-SA 4.0
2019-04-08T07:46:25.020Z
2019-04-08T07:46:25.020Z
benn
<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>

<rna-seq><figure-reproduction>
log2fold change as heatmap
# 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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