Request to support for issue facing in Ballgown

Question

[dikshapandey28]

Currently I am doing Differential Expression analysis of my data. I have used Hisat2, StringTie for alignment and quantification. My all results are good till output of StringTie, I got all .ctab files which required for Ballgown. But I am facing issue while creating ballgown object.

**

pheno_data = read.csv("/home/diksha/Downloads/pheno_data.csv")
bg <- ballgown(dataDir = data_directory, samplePattern="SRR", pData=pheno_data)

..

Error in ballgown(dataDir = data_directory, samplePattern = "SRR", 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 = data_directory, samplePattern = "SRR", 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...

Please help me to get fix this issue.**

[cpad0112]

did you check pData object in R and folder names?

dikshapandey28

[dikshapandey28]

pData object is getting NULL. And I ran the below command. It returning TRUE

all(pheno_data$Run == list.files("data_directory")) [1] TRUE

After this also, I am getting mentioned error.

[cpad0112]

could you please post contents of pheno_data and list.files(data_directory, pattern="SRR")here? @ dikshapandey28

In the mean time, please do following:

1) Change column name of the samples to "id" and condition column name as "group" (please note that these column names are not mandatory. I wanted to use id column in next command)

2) Sort the pheno_data sample column name alphabetically. For eg. pheno_data = pheno_data[order(pheno_data$id),]

3) Recreate the ballgown object.