DOC Degrees of freedom corner case#153
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BorisMuzellec merged 5 commits intomainfrom Jul 24, 2023
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Thanks @BorisMuzellec
LGTM.
pydeseq2/dds.py
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| The computation is based on genes whose dispersions are above 100 * min_disp. | ||
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| NB: when the design matrix has fewer than 3 degrees of freedom, the |
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NB can have different meanings. could you use NOTE: or something more explicit instead?
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What does your PR implement? Be specific.
As pointed out by @mikelove, in the corner case where the design matrix has fewer than 3 degrees of freedom, the distribution of log dispersions is poorly estimated by the MAD, as in
fit_dispersion_prior(cf the DESeq2 implementation ofestimateDispersionsPriorVar).This is a relatively minor issue that should be addressed in the future. Meanwhile, this PR:
fit_dispersion_priorto reflect this issue,