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How to generate a Venn diagram from edgeR DEG results?

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
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updated by Riku • Riku • written by Mehmet Mehmet

1 answer

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

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written by Gordon Smyth Gordon Smyth

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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written by Mehmet Mehmet

Sorry for replying on an earlier question.

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

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written by Riku • Riku

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