Hi there,
Lot of questions about DEXSeq today !
1) I would like to have some more informations about the meaning and the computation of the "exon usage coefficient" (mentionned in the page 15 of the tutorial) found in the DEXSeqResults object.
My guess is that it's somehow a combination of the relative exon usage and the size factor but I think I'm missing something.
2) How exactly is calculated the expression we see on the graph obtained with plotDEXSeq (first graph in the visualization part of the tutorial)? Is there a log transformation ? Is it related to this exon usage coefficient ?
3) Can DEXSeq results be interpreted out of the experiment context ? I mean, for a specific exon, can I take DEXSeq result (exon usage coefficient ? ) and divide by the exon length to have an idea of the general expression of this exon ?
4) I tried to use DEXSeq with three conditions. As results, I have only log foldchange between cond1 and the others, but nothing about cond2 vs cond3. Should I do something specific if I want all conditions to be tested together?
Lot of questions about DEXSeq today !
1) I would like to have some more informations about the meaning and the computation of the "exon usage coefficient" (mentionned in the page 15 of the tutorial) found in the DEXSeqResults object.
My guess is that it's somehow a combination of the relative exon usage and the size factor but I think I'm missing something.
2) How exactly is calculated the expression we see on the graph obtained with plotDEXSeq (first graph in the visualization part of the tutorial)? Is there a log transformation ? Is it related to this exon usage coefficient ?
3) Can DEXSeq results be interpreted out of the experiment context ? I mean, for a specific exon, can I take DEXSeq result (exon usage coefficient ? ) and divide by the exon length to have an idea of the general expression of this exon ?
4) I tried to use DEXSeq with three conditions. As results, I have only log foldchange between cond1 and the others, but nothing about cond2 vs cond3. Should I do something specific if I want all conditions to be tested together?