Ballgown error pData

[NDUFB11]

Hello everyone,
I'm facing a problem with ballgown that I'm not able to solve by my self ..

here the command that I use

pheno_data = read.csv(file ="phenotype.csv", header = TRUE, sep = ";")
samples <- c("sample1",sample2,.....sample8)
pf_rna<-ballgown(dataDir=file.path("ballgown/"), samplePattern = samples, pData=pheno_data)

and here is the output

Mon Jul 8 22:38:10 2019
Mon Jul 8 22:38:10 2019: Reading linking tables
Mon Jul 8 22:38:11 2019: Reading intron data files
Mon Jul 8 22:38:12 2019: Merging intron data
Mon Jul 8 22:38:14 2019: Reading exon data files
Mon Jul 8 22:38:16 2019: Merging exon data
Mon Jul 8 22:38:19 2019: Reading transcript data files
Mon Jul 8 22:38:19 2019: Merging transcript data
Error in ballgown(dataDir = file.path("ballgown/"), samplePattern = samples, :
first column of pData does not match the names of the folders containing the ballgown data.
In addition: Warning message:
In ballgown(dataDir = file.path("ballgown/"), samplePattern = samples, :
Rows of pData did not seem to be in the same order as the columns of the expression data. Attempting to rearrange pData...

Do you have any suggestion to why it doesn't like the pData?

Thank you

[sjm042]

1.can you show your "phenotype.csv"?
I doubt that your "phenotype.csv" make a mistake.
2.dataDir=file.path("ballgown/") =>dataDir="ballgown/" #that's my setting.

that's what i know.

[sjm042]

if it make sense ,tell me.thanks.
i learnning ballgown now.

[NDUFB11]

Hi sjm042,
Thank you for your response,
I deleted all the files because I want to start from the beginning.
I'm using the pipeline from the nature paper 2016 (hisat2,stringtie,ballgown) and right now I'm indexing the hisat2 genome.

I solved that issue by doing this:

#Read the design_matrix file
pheno_data = read.table(file ="phonotype.txt", header = TRUE, sep = "\t")
#full path to the sample directories
sample_full_path=paste("ballgown/",pheno_data[,1], sep = '/')
#Load ballgown data structure and save it to a variable “bg”
bg = ballgown(samples=as.vector(sample_full_path),pData=pheno_data)

I could solve also the previous problem by arranging the file names in the file.csv the same way as
appear on Rstudio (it's probably in alphabetic order)

Thanks again

[sjm042]

I use the same pipeline.