RNAseq analysis using EdgeR or Deseq2 for generating fold change graph
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12 weeks ago
najibveto ▴ 60

hello, I am trying to analyze RNAseq and I have table with genes and their read counts. for each conditions, we did triplicate. I would like to generate the fold change graph based on average log CPM instead of mean of normalized counts. I was thinking to use the plotmd for generating the graph, except i imported the data as deseq2 data. how is it possible to generate the graph using the deseq2 data?

change fold RNAseq • 252 views
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have a look into the manual (section "Log fold change shrinkage for visualization and ranking"). Is this what you want?

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thank you for the answer, I already generate the graph using Deseq2. I wanna generate fold change in function of log cpm using function plotmd from edgeR. I imported the table which contains count reads but can’t be used by plotmd.

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