How to generate a Venn diagram from edgeR DEG results?

Question

[Mehmet]

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.

Answer 1

[Gordon Smyth]

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

[Mehmet]

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()?

[Riku]

Sorry for replying on an earlier question.

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