Question: Ballgown plotTranscripts function
gravatar for Matina
3.5 years ago by
United Kingdom/University of Edinburgh
Matina160 wrote:

Hi everyone, 

I am using ballgown to measure transcript abundance in my RNA-seq samples. 
I want to plot the transcripts of a gene using the plotTranscript function of the ballgown package.

When i try to run:

plotTranscripts(gene='DDX11L1', gown=bg, samples='sample3_output',meas='FPKM', colorby='transcript', main='transcripts from gene DDX11L1: sample 3, FPKM')

I get this error:

    Error in seq.default(min(gtrans$start), max(gtrans$end), by = 1) : 
    'from' cannot be NA, NaN or infinite
    In addition: Warning messages:
    1: In min(gtrans$start) : no non-missing arguments to min; returning Inf
    2: In max(gtrans$end) : no non-missing arguments to max; returning -Inf

I have no clue about what it means. Until that point everything was executed without errors/warnings.

Any help would be much appreciated. 

plot rna-seq trancript ballgown R • 1.7k views
ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by Matina160


i have not used this s/w but it seems that there are missing values in the Transcript Strt/End coords. Or/ also somehow End -Strt is not being equal to/ > 1.

I suggest that if you have the result file in text format, then grep out the lines for your gene and check if the Strt, End pos. & FPKM values seem fine.

Also, a long shot, but also check if you have not switched between genome releases (GRCh37 to GRCh38 or vice versa) at any point. Cant be more specific as I have not used ballgown but the above checks are a good starting point.

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by Amitm1.6k

Thanks a lot for the reply Amitm. 

The solution is a lot simpler and is basically my mistake. Instead of the gene name I had to use the ensembl gene_id. Thats why it coudnt find the ranges. 

ADD REPLYlink written 3.5 years ago by Matina160
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1314 users visited in the last hour