Hi. I am using ballgown to support my reading analysis with Cufflinks as well as set up phenotype data for RSEM later. I was looking it up on Google and nobody seemed to have an answer with most of the questions being ignored.

The error comes from this:

bg_HNSCC = ballgown(dataDir = "ballgown", samplePattern = "ERR", pData=pheno_data)

which results in:

Mon Sep 11 17:50:00 2023
Mon Sep 11 17:50:00 2023: Reading linking tables
Error in file(file, "rt") : invalid 'description' argument

I have checked and I am in the ballgown directory which the pheno_data is in. Also the pheno_data contains:

ID,Disease,HPVSTAT,PART
ERR2707349,normal,HPVNEG,tonsil
ERR2707350,normal,HPVNEG,tonsil
ERR2707351,normal,HPVNEG,tonsil
ERR2707352,normal,HPVNEG,tonsil
ERR2707357,HNSCC,HPVNEG,tonsil
ERR2707358,HNSCC,HPVNEG,tonsil
ERR2707359,HNSCC,HPVNEG,tonsil
ERR2707360,HNSCC,HPVNEG,tonsil

I have been trying to find a solution for a while but can't find anything.