Gene enrichment analysis R studio error

Question

[iamsmor]

Hi everyone

I started gene enrichment analysis but I am started with R error mentioned below.

> library(clusterProfiler) library(GSEABase) library(org.Hs.eg.db)
> filename<- "c7.all.v7.1.entrez.gmt" gmtfile <- system.file(filename)
> c6 <- read.gmt(gmtfile)

I get error

> Error in stack.default(res) : at least one vector element is required
In addition: Warning message:
In file(con, "r") :
  file("") only supports open = "w+" and open = "w+b": using the former

What should I do for it? Thank you

Answer 1

[Thomas]

This error is raised when the file exists but is empty, so you need to check that your file isn't empty. Note that if the file is in a folder that's synchronizing to a cloud solution that lets you decide whether a file is only in the cloud or always stored locally and you selected cloud, the file will appears as if it exists in the file system, but is actually empty (this happened to me with Nextcloud). The solution then is to make sure the file is downloaded and present on your local device.