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Question: Algorithm behind splice=TRUE in DEXSeq
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gravatar for cwt_kiwi
7 weeks ago by
cwt_kiwi0
cwt_kiwi0 wrote:

Hello everyone,

there is a plot function in DEXSeq, by which you can plot the exon usage per exon (fitted splicing). I know how to plot this already. The question is, does anyone know how this "Exon usage" is calculated exactly? How was the "overall changes in gene expression" defined or calculated in DEXSeq? And can I find or generate this information in/from the DEXSeq Result Table? 

Also, could anyone explain, if there's any difference in terms of the concepts and the application of the calculated "differential exon usage" in DEXSeq and the also very popular "PSI-analysis"? And what are the pros and cons?

Thank you very much for your attention of this post. You answer will be highly appreciated.

ADD COMMENTlink modified 7 weeks ago by Alejandro Reyes1.5k • written 7 weeks ago by cwt_kiwi0
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gravatar for Alejandro Reyes
7 weeks ago by
Alejandro Reyes1.5k
Dana-Farber Cancer Institute, Boston, USA
Alejandro Reyes1.5k wrote:

Hi, the details of the estimation of exon fold changes is described in the DEXSeq paper. The "overall gene expression" can not be extracted from the DEXSeq results, but if you are interested in changes in gene expression it is better to look at packages like DESeq2, etc.

I have not done a very systematic comparison between exon fold changes and PSI. But I can tell you that for differentially used exons, the exon fold changes and the delta PSIs will be strongly correlated. 

ADD COMMENTlink written 7 weeks ago by Alejandro Reyes1.5k

Dear Mr. Reyes,

thank you very much for your reply. Would it be possible to extract the result of the "Relative Usage of Exon", which is the y-axis of the fitted splicing plot?

ADD REPLYlink written 7 weeks ago by cwt_kiwi0
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