Question: ballgown error: Rows of pData did not seem to be in the same order as the columns of the expression data.
0
gravatar for jolin0701-dy
2.3 years ago by
jolin0701-dy70
jolin0701-dy70 wrote:

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..

rna-seq R • 2.8k views
ADD COMMENTlink modified 21 months ago by 58483973310 • written 2.3 years ago by jolin0701-dy70

Looks fine. Can you confirm that the data directory name and location is accurate? You can try samplePattern="" without pData = pheno_data.

Best

ADD REPLYlink written 2.3 years ago by Satyajeet Khare1.3k
1
gravatar for 584839733
21 months ago by
58483973310
58483973310 wrote:

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

ADD COMMENTlink written 21 months ago by 58483973310
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