I am using my data to follow the tutorial - Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification.
When I run:
all(rownames(cts) %in% txdf$TXNAME)
It gives FALSE rather than TRUE.
I have checked that all row names are unique in my salmon quantification files by running:
dups <- which(duplicated(Dem1rep1.quant)) unique(Dem1rep1.quant[dups]) length(dups)
This gave zero duplicates for all of the quantification files.
What could be causing my error? If I ignore the error and continue with the workflow I get this error when running:
d <- dmDSdata(counts=counts, samples=samps) Error in dsDSdata(counts=counts, samples=samps) : sum(duplicated(counts$feature_id)) == 0 is not TRUE
Any help would be greatly appreciated