Implement fitType="mean" for vst #123
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scottgigante-immunai
requested review from
BorisMuzellec,
maikia and
arthurPignetOwkin
as code owners
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@BorisMuzellec this is failing because IPython no longer supports Python3.8, unrelated to my PR. Leaving it to you to write tests to compare performance here to the R version. |
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Thanks for this PR @scottgigante-immunai! I'll try to find some time this week to fix the issue with IPython and write some R / Python tests. |
BorisMuzellec
approved these changes
May 10, 2023
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Just implemented tests to compare with DESeq2, seems all good! Thanks @scottgigante-immunai! I'm merging this PR
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Amazing! Thanks @BorisMuzellec |
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Closes #116.
DESeq2 has a fit type "mean" for the vst which is used as the fallback when the parametric fit fails. It would be nice to have an equivalent in the python implementation.
Here's my attempt based on https://github.com/mikelove/DESeq2/blob/devel/R/vst.R#L188 and https://github.com/mikelove/DESeq2/blob/devel/R/core.R#L892 .
No guarantees that it's exactly the same -- I'm not really familiar enough with the algorithm to dive much deeper.