tximport error
1
0
Entering edit mode
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
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$infReps)  I have checked the folder and abundance files of the two missing samples, the look like other samples, nothing different dose anyone know what is going on? error tximport • 231 views ADD COMMENT 0 Entering edit mode @mikelove Last seen 20 hours ago United States Do you get the error on the first few samples (e.g. 1-3)? How do you obtain the txi if there is an error? It should not be returning a txi object. What if you run it on samples 12-13 only? ADD COMMENT 0 Entering edit mode I don't know how I have the txi, but I have it and I get this error with it too. I tried adding this argument dropInfReps =T and now I don't get any errors. what does this argument do? and now names(txi$infReps) returns NULL

0
Entering edit mode

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