Joint disperstion estimation for DEXSeq and DESeq2
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@kvittingseerup-7956
Last seen 5 days ago
European Union

Since DEXSeq::estimateDispersions() and DESeq2::estimateDispersions() are often the most time-consuming step of the two pipelines I was wondering if it was possible to share the result of this between a (naturally paired) DTE and DTU analysis using DESeq2 and DEXSeq respectively or if they are indeed different?

Cheers

Kristoffer

DESeq2 DEXseq • 103 views
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@mikelove
Last seen 23 hours ago
United States

hi Kristoffer,

They are indeed different because the DTU model additionally shares coefficients and therefore conditional expected values of counts within gene, whereas DTE looks at each transcript on its own.

An idea for speeding up these models is to see to what extent you can use fitType="glmGamPoi". I think it should work out of the box for DTE, but may need some backend work for DTU. glmGamPoi should work well when you have a moderate to high number of samples, whereas the standard DESeq2 dispersion fitting is most important for low to moderate sample size.

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Hi Mike

Thanks - just wanted to be sure. I did look for fitType="glmGamPoi" in DEXSeq but could not find it. If you can find time to implement it that would be awesome(!) - but naturally understandable if you cannot :-)

Cheers Kristoffer

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Ah yeah it's only in DESeq2. I'm not a DEXSeq devel, but maybe someone from that side could attempt it at some point.