Hi everyone, I am using ballgown to do differential gene expression analysis. But I have a question about the pData file. I am not sure what information should be included in phenotype files. I have four datasets, which are two replicates for two samples. Here is the phenotype files I generated. sample1 sample2 sample3 sample4 e_data_ctab e_data_ctab e_data_ctab e_data_ctab e2t.ctab e2t.ctab e2t.ctab e2t.ctab i_data.ctab i_data.ctab i_data.ctab i_data.cta i2t.ctab i2t.ctab i2t.ctab i2t.ctab t_data.ctab t_data.ctab t_data.ctab t_data.ctab
I also used codes below: pDATA(bg)=data.frame(id=sampleNames(bg),group=rep(c(0,1),each=2)) But I am still getting error when I ruined stattest Error in stattest(bg_2, feature = "transcript", meas = "FPKM", covariate = "group") : to do statistical tests, either gown must contain pData or you must specify models. I am new to R language so I don't know how to troubleshoot this problem. Can someone help me out? I really appreciate your help. Thank you.