Question: Ballgown plotTranscripts function
0
gravatar for Matina
3.1 years ago by
Matina160
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 • 1.5k views
ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by Matina160

hi,

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 3.1 years ago • written 3.1 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 3.1 years ago by Matina160
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