How can I use UpSet plot for expression/RNA-seq data
You need to generate a list of gene ID vectors to feed into upset. In the example below, I am selecting observations (genes) which have an level above the median level. You could also choose only genes above the 3rd quartile, etc. You then need to convert these from a list of character vectors to a presence/absence matrix. UpSetR has a fromList function that does just this.

In future, be more specific about what you want to achieve and supply example data for people to work with.

library("UpSetR")

tmp &lt;- mtcars

tmp$car &lt;- rownames(mtcars)
list &lt;- lapply(colnames(mtcars), function(x) {
  tmp[tmp[[x]] &gt; median(tmp[[x]]), "car"]
})
names(list) &lt;- colnames(mtcars)

upset(fromList(list))




Created on 2019-10-17 by the reprex package (v0.3.0)