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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.

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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.

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  • $\begingroup$ 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 . $\endgroup$ – krushnach Chandra Apr 8 '19 at 9:25

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