[BioC] DESeq vs DEXSeq

[Robert M. Flight]

We have a biological system where we are interested in finding
differential expressed exons (on a genome basis) between conditions,
and are wondering whether it is more appropriate to use DESeq or
DEXSeq for the analysis. Have RNASeq data on three conditions.

>From my understanding of the two packages, DESeq (and alternatively
edgeR) allow testing for diff. expression of any object one can define
counts for, whereas DEXSeq looks for genes (however defined) where
there are only one or a few exons that show differential expression.

My initial belief was that DEXSeq was the best choice, however we are
working with data from Rat, which has rather poorly annotated exons,
especially in non-coding regions (i.e. UTRs). Therefore, I am thinking
of defining exons based on a combination of the current annotation,
known UTRs, and exons assembled by CuffLinks. I am not sure how this
set of exons would fit into DEXSeq, and it seems to me that DESeq
would be more appropriate, with determination after DE analysis to
determine exon location (CDS, UTR, etc).

I would appreciate insights or experiences others have had.

Regards,

-Robert

Robert M. Flight, Ph.D.
University of Louisville Bioinformatics Laboratory
University of Louisville
Louisville, KY

PH 502-852-1809 (HSC)
PH 502-852-0467 (Belknap)
EM robert.flight at louisville.edu
EM rflight79 at gmail.com
robertmflight.blogspot.com
bioinformatics.louisville.edu/lab

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