Error and warning message when reading the ballgown object
1
0
Entering edit mode
amy16 • 0
@amy16-14425
Last seen 3.1 years ago

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

software error illumina DEG ballgown tuxedo • 925 views
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 1 day ago
United States

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?

ADD COMMENT
0
Entering edit mode

I checked the i_data.ctab files and found that the ids are different. So, is there anything I can do to fix it?

-Amy

ADD REPLY
0
Entering edit mode

I too am facing similar issue where I am trying to load control and sample together to extract the differentially expressed genes in ballgown but I get same error as the iid is different for controls and samples in idata.ctab. Any help on this please?

ADD REPLY

Login before adding your answer.

Traffic: 191 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6