Hi, I am trying out the new tuxedo protocol (hisat, stringtie and ballgown). While calling the ballgown function with

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

I get

Error in file(file, "rt") : invalid 'description' argument

Any help in this regard would be appreciated.

Thanks in advance :)

Hi there, this error usually means something went wrong with trying to read in the pData argument. The error comes from read.table, not from ballgown. More detail would be helpful in debugging here:

* what is "pheno_data" in your example? (is it a file path?)
* what are the contents of the file in that path?
* what happens when you try to read in whatever the pheno_data file is with read.table or read.csv? 

If you can get pheno_data file read in with a different function beforehand (read.table or read.csv), you can pass the resulting data frame directly to the ballgown function. But this error is coming from read.table, so if you solve that problem you will solve this one.

Hope that helps!