I have analyzed gene expression of Arabidopsis by RNA-seq data and now I try to use "ballgown" to examine the difference of expression of transcripts, but I have a problem how to use "ballgown".

I have 36 dataset: 2 organs, 4 time points for each organ, 2 types of light treatment for each time point of each organ and 2 replicates, 2*4*2*2=32, and 2 organs, 1 time points for each organ, 1 types of light treatment for each time point of each organ and 2 replicates, 2*1*1*2=4, 36 conditions in total. I calculated the expression of transcripts for each condition along a protocol about RNA-seq analysis using "HISAT2", "Stringtie" and "ballgown" listed in Nature Protocols. And, I practiced the following scripts by R to visualise the difference of expression of transcripts;

> pheno_data <- read.csv("phenodata.csv")

#    ids    Light    TP

#    TP0_01    White    0

#    TP0_02    White    0

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

#Fri Oct 21 14:10:20 2016
#Fri Oct 21 14:10:20 2016: Reading linking tables
#Fri Oct 21 14:10:22 2016: Reading intron data files
#Fri Oct 21 14:11:22 2016: Merging intron data
#Fri Oct 21 14:11:28 2016: Reading exon data files
#Fri Oct 21 14:13:31 2016: Merging exon data
#Fri Oct 21 14:13:38 2016: Reading transcript data files
#Fri Oct 21 14:14:14 2016: Merging transcript data
#Error in ballgown(dataDir = "ballgown", samplePattern = "TP", 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 = "TP", 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...

Then, I got the above error. In this case, how can I deal with this problem? I want to know what went wrong in this script. I hope if you could tell me.

Thanks for your time if you've red this whole novel of a post.

Here is the error you got:

first column of pData does not match the names of the folders containing the ballgown data.

Which seems pretty self explanatory to me. There are expectations on the format of the pData object, and yours does not conform. So you either have to make sure that the first column of the pData object matches the name of the folders containing the ballgown data, OR choose the easier route and call ballgown without specifying the pData, which seems the better of the two choices.