How to generate a Venn diagram from edgeR DEG results?
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3.0 years ago
Mehmet ▴ 820

Dear All, I have done DEG analysis of genes from 4 samples using edgeR. I want to plot them (number of DEGs) using a Venn diagram. I have results from pairwise comparisons as UP and DOWN gene list with additional parameters that are generated by edgeR. Is there a way to prepare data from edgeR results and generate a Venn diagram in R? I am confused at data preparation for input in R.

Thank you in advance.

R edgeR RNA-seq Venn diagram • 2.3k views
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3.0 years ago
Gordon Smyth ★ 7.7k

The vennDiagram() function produces Venn diagrams directly from the edgeR decideTests() output.

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Thanks for your reply. But I have DE gene list from 4 samples only in the format below:

sampleA sampleB logFC   logCPM  PValue  FDR

and how can I prepare them for decideTests()?

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Sorry for replying on an earlier question.

I have the same problem. Could you tell me how you solved it?

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