I plan to use the readDGE function with two CSV files containing gene counts from different samples. One has 2814 genes and the other 2809 genes. The files are on my Desktop and this is the error that I get: 

> files <- dir(pattern="*\\.csv$")

> 
> RG <- readDGE(files)
Error in `[.data.frame`(d[[i]], , columns[2]) : 
  undefined columns selected
> 

How I can fix the error?

readDGE expects that each file is tab-separated and contains at least two columns (one of gene names/IDs and another of gene counts). It seems that your files do not follow this format, i.e., fewer columns than expected. This is probably because a different separator is involved - for CSV files, you should set sep="," in the readDGE call, as is mentioned in the documentation for the function. Also see the columns argument in ?readDGE if there are more than two columns and the first two do not correspond to the IDs and counts.

There a few problems here:

First, as already noted, you need to specify sep="," because you have a comma-separated file.

Second, there is a problem with your files. Somewhere in one of your data files you have a character entered where you should have a number. Have a look especially at the last row of your files, as that is often the culprit. Check that your files don't contain any unnecessary spaces, because a space will be read as a character.

Third, you only have two samples in total, meaning the sample size is n=1 in each group. In other words you have no replication. So there isn't much analysis that edgeR will be able to do for you, because edgeR is designed to work with biological replicates.