was wondering if somebody could explain how limma produces genes that will be entered in to a venndiagram. I have produced a vennDiagram using limma results:
resultsvennliversamples <- decideTests(ebayesliversamples, method="separate", adjust.method="BH", p.value=0.05)
then call vennDiagram to look at the result. This is really nice, however, I get a different number of genes when I then change the "include" argument.
For "both" up-regulated and down-regulated genes, I get (just as an example) 168 genes on one outer ring (specific to one contrast).
Now, if I ask for genes that are up-regulated only (include="up") then the same outer ring as above now contains 301 genes. Similarly, include= "down" = 174 genes.
This is really confusing for me, as I thought there should be 168 genes in total and then the up and down regulated genes would be a number out of the 168...
My question is, why, when specifying to view genes that are specifically up-regulated or down-regulated, are there more genes than the total number of DE genes exclusive to this contrast when specifying "both"
Not sure of the code that might be useful here, I also couldn't directly attach the venn diagrams, however, I will respond with any requests for further code etc! But any help with this would be greatly appreciates as it is incredibly confusing!