This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Ballgown plotTranscripts function

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.

ballgown trancript r plot rna-seq
• 3,800 views • link
updated by Ram Ram • written by Matina Matina

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.

• 0 views • link
updated by Ram Ram • written by Amitm Amitm

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. That's why it coudnt find the ranges.

• 0 views • link
updated by Ram Ram • written by Matina Matina

0 answers

No answers yet.

Log in to answer this question.

More posts like this