Question: Error while loading the data structrure in the ballgown tool
0
gravatar for Mithil Gaikwad
10 weeks ago by
Tezpur University, India
Mithil Gaikwad0 wrote:

Hello, I am facing an error while loading my data structure in ballgown tool,  I have triedfollowing are the commands which i am using in my data:

>setwd("/Users/kchougul/data/testdata/Ballgown/tutorial_example")
>library(ballgown)
>library(ggplot2)
>library(gplots)
>library(genefilter)
>library(GenomicRanges)
>library(plyr)
>pheno_data = read.csv(file ="design_matrix", header = TRUE, sep = ",")
>sample_full_path <- paste("SRRXXX", "SRRYYY", "SRRZZZ",pheno_data[,1], sep = ',')

#SRRXXX, SRRYYY are my ballgown folders containing respective SRRXXX.gtf and SRRYYY.gtf files

>bg = ballgown(samples=as.vector(sample_full_path),pData=pheno_data)

Tue Nov 13 13:13:27 2018
Error in ballgown(samples = as.vector(sample_full_path), pData = pheno_data) :

Something is wrong: are you missing .ctab files? Do extra files/folders (other than tablemaker output folders) match your samples/dataDir/samplePattern argument(s)?

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