AIC-like measure for DESeq2
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@jonathan-cairns-6949
Last seen 7.5 years ago
Cambridge, UK

Hi,

I am experimenting with the use of size factors in DESeq2 (i.e. the s_ij factors). Essentially, I would like to show that the use of gene-specific s_ij factors, derived from external data, improves the model's fit.

Is there a simple way to derive an AIC-like measure from my DESeq2 object for this purpose? Or perhaps there is a better method to do this?

Apologies if this has been answered before - I couldn't find anything appropriate.

Thanks,

Jonathan

deseq2 • 1.4k views
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@mikelove
Last seen 23 hours ago
United States

You could look at the likelihood with different size factor vectors. You can put in arbitrary size factors with sizeFactors(dds) <- ... before running DESeq(). In the mcols(dds) after running DESeq() you can find the deviance which is -2 * log likelihood.

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Thanks - I will look at the total deviance.

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@wolfgang-huber-3550
Last seen 12 weeks ago
EMBL European Molecular Biology Laborat…

You could use cross-validation: fit the model on a subset of the samples,  then apply to the held-out samples and show that prediction performance on these increases.

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