> library(ballgown)

Attaching package: ‘ballgown’

The following object is masked from ‘package:base’:

    structure

> pheno_data=read.csv("C:/pheno_data/PSC3_phenodata.csv")
> bg_PSC=ballgown(dataDir=("C:/ballgown"),samplePattern="PSC", pData=pheno_data)
Sun Jul 08 17:56:17 2018
Sun Jul 08 17:56:17 2018: Reading linking tables
Sun Jul 08 17:56:19 2018: Reading intron data files
Sun Jul 08 17:56:36 2018: Merging intron data
Sun Jul 08 17:56:41 2018: Reading exon data files
Sun Jul 08 17:57:38 2018: Merging exon data
Sun Jul 08 17:57:46 2018: Reading transcript data files
Sun Jul 08 17:58:19 2018: Merging transcript data
Error in ballgown(dataDir = ("C:/ballgown"), samplePattern = "PSC", pData = pheno_data) :
  first column of pData does not match the names of the folders containing the ballgown data.
In addition: Warning message:
In ballgown(dataDir = ("C:/ballgown"), samplePattern = "PSC", pData = pheno_data) :
  Rows of pData did not seem to be in the same order as the columns of the expression data. Attempting to rearrange pData...
> save.image("C:\\pheno_data\\Ballgown_PSC1.RData")
>

When I use list to look at my loaded _phenodata.csv in R, I see 1st column is 1-38, my samples. 2nd column is the name of the sample dir from my stringtie -e -B  -G _merged.gtf file in my ballgown dir. How do i solve this trivial issue. Thanks for some help. steve  Above is a copy of the i ballgown error. steve