tximport error
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hana • 0
@a8af0389
Last seen 9 weeks ago
United States

I am using tximport to import abundance.tsv file from kalisto and I get this error:

Note: importing `abundance.h5` is typically faster than `abundance.tsv`
reading in files with read_tsv
1 2 3 4 5 6 7 8 9 10 11 12 13 
transcripts missing from tx2gene: 1
summarizing abundance
summarizing counts
summarizing length
Error in rowsum.default(x[sub.idx, , drop = FALSE], geneId) : 
  incorrect length for 'group'

it seems that it is reading my 13 sample tsv file but apparently only 11 of them are in the tximport object when I check the infReps

names(txi$infReps)

I have checked the folder and abundance files of the two missing samples, the look like other samples, nothing different dose anyone know what is going on?

error tximport • 231 views
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@mikelove
Last seen 20 hours ago
United States

Do you get the error on the first few samples (e.g. 1-3)?

How do you obtain the txi if there is an error? It should not be returning a txi object.

What if you run it on samples 12-13 only?

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I don't know how I have the txi, but I have it and I get this error with it too. I tried adding this argument dropInfReps =T and now I don't get any errors. what does this argument do? and now names(txi$infReps) returns NULL

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It reads in bootstrap replicates. Maybe you ran the 13 files differently?

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