After running the
dex.padj <- getAdjustedPValues(stageRObj, order=FALSE, onlySignificantGenes=TRUE), and filtering for only the transcripts in the final table that are less than 0.05 I received a list of genes with only 1 transcript that was significant.
I was curious to see what the expression of this gene looked like in relation to the 1 transcript that was found to be significant. Using the
tximport I was surprised to see that in many cases there were other transcripts that maybe should have been considered DTU as well...
geneID txID gene transcript ENSG00000006468 ENST00000485475 7.875795e-06 1.402172e-06 ENSG00000006468 ENST00000483075 7.875795e-06 3.333497e-01 ENSG00000006468 ENST00000405192 7.875795e-06 6.832075e-01
A graph of expression, can be found here: https://www.dropbox.com/s/52vpnqroxk88h3y/ENSG00000006468.pdf?dl=0
As a side note, what would be considered the minimum read depth for DTU detection?