Joint disperstion estimation for DEXSeq and DESeq2
1
0
Entering edit mode
@kvittingseerup-7956
Last seen 7 months 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 • 1.0k views
ADD COMMENT
3
Entering edit mode
@mikelove
Last seen 15 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.

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 769 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6