Error in ballgown(dataDir = "ballgown", samplePattern = "ERR", pData = pheno_data) :s.null(pData) | class(pData) == "data.frame" are not all TRUE

[aaubry89]

Hi,

I apologize if this is the wrong place to ask this question or if it's been asked already but I am having an issue with ballgown. I'm trying to perform the analysis on data that is associated with the Pertea et al, 2016 nature protocol paper. My issue is with step 9. Here Is my code

library(ballgown) library(RSkittleBrewer) library(genefilter) library(dplyr) library(devtools) pheno_data <-read.csv("geuvadis_phenodata.csv") bg_chrX = ballgown(dataDir = "ballgown", samplePattern = "ERR", pData = pheno_data)

The error I get is Error in ballgown(dataDir = "ballgown", samplePattern = "ERR", pData = pheno_data) : is.null(pData) | class(pData) == "data.frame" are not all TRUE

However if I run all(pheno_data$ids ==list.files("ballgown")) I get TRUE. So I'm a bit confused. Any help is appreciated.

[sjm042]

make sure that your datadir is right.
make sure that you have run this command : pheno_data = read.csv("pheno_data_X.csv")