I have a time course experiment with two conditions, control and treatment, with three biological replicates for each time point except for time 0 (control conditions) that has two biological replicates. I'm using the pipeline of "Hisat, strong tie, ballgown) for data analysis. I have the problem with ballgown.
ballgown directory contains 11 folder corresponding to 11 samples (from the string tie output) and the data_form.csv file . The name and order of folders are the same as .csv file. There are 5 files ending to .ctab in each folder.
setwd ("E:/sequencing/ballgown") data_form = read.csv ("data_form.csv") data_form ids treatment time sample1 control 0 sample2 control 0 sample3 drug 2 sample4 drug 2 sample5 drug 2 sample6 drug 12 sample7 drug 12 sample8 drug 12 sample9 drug 24 sample10 drug 24 sample11 drug 24
sample=c("sample1","sample2","sample3","sample4","sample5","sample6","sample7","sample8","sample9","sample10","sample11") But with the below command, I get the error: bg = ballgown(dataDir = "ballgown", samplePattern = "sample", pData = data_form) Error in file(file, "rt") : invalid 'description' argument
I searched on the net and saw the similar error, but it's not helpful for me. Could you please help me to solve this problem? I'm very grateful if you kindly tell me how to define two biological replicates for control (time 0) and three replicates for other times in ballgown?
Thank you in advance.