I am following Michael Love's tutorial: "Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification" for DTU analysis.
Having some issue with setting it up for DRIMSeq, I am getting this:
> all(rownames(cts) %in% txdf$TXNAME)
all(rownames(cts) == txdf$TXNAME)
Not sure how to fix that?
Assuming the above is leading to this issue when putting this command:
d <- dmDSdata(counts=counts, samples=samps)
It's coming back with error saying: all(samples$sample_id %in% colnames(counts)) is not TRUE
I can tell that my sample id's does not match the column sample id's, for example, sample id's are in this format: '780-med', and colnames(counts) is 'X780.med'
Would anyone know how to fix the two issues? Thank you in advance!