I'm trying to use DEXSeq on RNA-seq data. There is one gene I know is supposed to have differential exon usage, because a few of the exons were knocked-out.
When I look at the data of this gene I see a beautiful plot that suggests differential splicing (as expected, see attached figure), and also very good p-values for differential splicing in several of the exon (see attached figure). However, the padj values are all NA.
I suspect that there is some filtering that is taking place, but I do not know how to control it.
Weizmann Institute of Science