[BioC] DESeq vs DEXSeq

Robert M. Flight rflight79 at gmail.com
Mon Mar 26 17:29:39 CEST 2012

Thanks Simon, that was a really useful explanation of how we might
want to go about it.


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

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discoveries, is not "Eureka!" (I found it!) but "That's funny ..." -
Isaac Asimov

On Mon, Mar 26, 2012 at 10:52, Simon Anders <anders at embl.de> wrote:
> Dear Robert
> On 03/26/2012 04:26 PM, Robert M. Flight wrote:
>>> 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.
> The crucial difference between DESeq and DEXSeq is that the latter aims to
> tease apart changes to the overall expression strength of a gene and changes
> to only some of its exons. Conceptionally, we consider the for each sample
> the fraction "number of reads overlapping with the exon (or: counting bin)
> under consideration" over "number of reads mapping to any exon of the gene".
> If the gene's overall expression changes but the relative abundances of the
> different transcripts stay the same, these fractions do not change, and
> DEXSeq will not call this counting bin significant even if its absolute
> count does change significantly.
> (Note that this is a simplified explanation of what DEXSeq does
> conceptually. To see what it actually does, please see our preprint on
> Nature Precedings.)
>> 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).
> Once you have defined exons on a combination of information you trust, you
> can use DEXSeq. All you need is a table of counts, one column for each
> sample and one row for each exon -- or for whatever counting bins you want
> to define: It may be useful, for example, to keep the UTR and the coding
> part of outer exons separate. Then, define a factor to indicate which rows
> belong to the same gene and use this to call 'createExonCountSet'.
>  Simon
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