I'm using ballgown to analyze the data and got an error.

> pheno_data <- read.table(pheno_data_file, sep="\t", header=T)

> pheno_data

Samples	Group

Sample_male_1	Group1

Sample_male_2	Group1

Sample_male_3	Group1

Sample_female_1	Group2


Sample_female_2	Group2

Sample_female_3	Group2

> bg <- ballgown(dataDir = "ballgown", samplePattern="Sample", pData=pheno_data)

Wed Dec 21 10:36:10 2016

Wed Dec 21 10:36:10 2016: Reading linking tables

Wed Dec 21 10:36:15 2016: Reading intron data files

Wed Dec 21 10:36:32 2016: Merging intron data

Wed Dec 21 10:36:37 2016: Reading exon data files

Wed Dec 21 10:37:17 2016: Merging exon data

Wed Dec 21 10:37:24 2016: Reading transcript data files

Wed Dec 21 10:37:41 2016: Merging transcript data

Error in ballgown(dataDir = "ballgown", samplePattern = "Sample", 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 = "ballgown", samplePattern = "Sample", 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...

Execution halted

It seems that the order in phone_data should be exactly the same in the folder of ballgown.

Any help would be greatly appreciated..
hi
I recently got the same err.through reading the protocal,I find a solution:
To make sure that the file names match the
IDs in the phenotype file, run the following
R command:
> all(pheno_data$ids == list.
files("ballgown"))

I guess your pheno_data's order maybe not match the sample file order.
You can reorder your pheno_data_file's Samples as `list.
files("ballgown"))` to solve this problem.

Best