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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.

Mati
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  • Did you spellcheck the function arguments? Anything else is hard to say without a [reproducible example](http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example) – Heroka Feb 06 '16 at 17:17

2 Answers2

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it seems to need gene_id rather than gene_name Column 9 from the file t_data.ctab

Paula Andrea
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Indeed, you should use the geneID, which look like MSTRG.13518, instead of gene name. However, in description of the function the argument gene should be the "name of gene whose transcripts will be plotted. When using Cufflinks output, usually of the form "XLOC_######" "

I think that this is is some kind of bug and I'll ask developers is that what they meant.

Vitaly
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