Hi,

I am using Ballgown as apart of the tuxedo suite for DEG, and I get this warning message while reading the ballgown object,

> pheno_data01<-read.csv("/fast/a123456/Analysis02/DGE/prr01/prr01.csv")
> bg<-ballgown(dataDir="/fast/123456/Analysis02/DGE/prr01", pData=pheno_data01, samplePattern="B")
Sun Apr  8 10:15:20 2018
Sun Apr  8 10:15:20 2018: Reading linking tables
Sun Apr  8 10:15:22 2018: Reading intron data files
Sun Apr  8 10:15:30 2018: Merging intron data
Error in ballgown(dataDir = "/fast/123456/Analysis02/DGE/prr01",  :
  intron ids were either not the same or not in the same order across samples. double check i_data.ctab for each sample.
In addition: Warning messages:
1: In x$i_id != intronAll[[1]]$i_id :
  longer object length is not a multiple of shorter object length
2: In x$i_id != intronAll[[1]]$i_id :
  longer object length is not a multiple of shorter object length
3: In x$i_id != intronAll[[1]]$i_id :
  longer object length is not a multiple of shorter object length
4: In x$i_id != intronAll[[1]]$i_id :
  longer object length is not a multiple of shorter object length
5: In x$i_id != intronAll[[1]]$i_id :
  longer object length is not a multiple of shorter object length
6: In x$i_id != intronAll[[1]]$i_id :
  longer object length is not a multiple of shorter object length

The pheno_data01 in csv file is as follows:

ids,treatment,genotype
B1C_01,control,resistant
B1C_02,control,resistant
B1C_03,control,resistant
B1C_04,control,resistant
B2C_01,control,susceptible
B2C_02,control,susceptible
B2C_03,control,susceptible
B2C_04,control,susceptible

please advise me on how I fix this error.

Thanks in advance

-Amy

I think you already got the advice you need:

Error in ballgown(dataDir = "/fast/123456/Analysis02/DGE/prr01",  :
  intron ids were either not the same or not in the same order across samples. double check i_data.ctab for each sample.

Did you check the i_data.ctab file for each sample?