I'm using ballgown to analyze the data and got an error.
pheno_data <- read.table(pheno_data_file, sep="\t", header=T)
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...
It seems that the order in phone_data should be exactly the same in the folder of ballgown.
Any help would be greatly appreciated..