Hello,

I have an error that I can't resolve when I'm creating a ballgown object:

> pheno_data = read.csv("HighLow_phenodata_2.csv", sep=";", header=T)
> bg = ballgown(dataDir = "ballgown", samplePattern = "SNBN", pData=pheno_data)

Thu Jun  1 17:38:29 2017
Thu Jun  1 17:38:29 2017: Reading linking tables
Thu Jun  1 17:38:29 2017: Reading intron data files
Thu Jun  1 17:38:30 2017: Merging intron data
Thu Jun  1 17:38:30 2017: Reading exon data files
Thu Jun  1 17:38:31 2017: Merging exon data
Thu Jun  1 17:38:31 2017: Reading transcript data files
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  scan() attendait 'a real' et a reçu '.'

> traceback()
4: scan(file = file, what = what, sep = sep, quote = quote, dec = dec, 
       nmax = nrows, skip = 0, na.strings = na.strings, quiet = TRUE, 
       fill = fill, strip.white = strip.white, blank.lines.skip = blank.lines.skip, 
       multi.line = FALSE, comment.char = comment.char, allowEscapes = allowEscapes, 
       flush = flush, encoding = encoding, skipNul = skipNul)
3: read.table(file, header = TRUE, sep = "\t", colClasses = cc, 
       quote = "")
2: .readTranscript(f, meas)
1: ballgown(dataDir = "ballgown", samplePattern = "SNBN", pData = pheno_data)

If anyone has an idea to solve it or know a package to do gene expression analysis like ballgown :/

Thank you !

I fund what was the problem. For those who would have this problem:
- I used a gtf file that I created alone
- it was the source of the problem because of the last column

For a GTF file, the values in the last column must be spaced because the columns are separated by tabs.
When generating a GTF file, I had everything tabbed, that's why the scan problem!

If it is csv file, why is sep semicolon?

"HighLow_phenodata_2.csv", sep=";"

My excel software put ";" but i try with "," and i also get the error :/