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Clarify design formula and blind dispersion estimation #1367

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merged 3 commits into from
Sep 3, 2024
Merged

Clarify design formula and blind dispersion estimation #1367

merged 3 commits into from
Sep 3, 2024

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pmoris
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@pmoris pmoris commented Aug 29, 2024 •
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I think it could be useful to explicitly mention what the design formula ~1 is doing (= specifying an intercept-only model) and how this relates to the dispersion estimation that happens during the variance stabilizing transformation (= the default argument of both rlog and vst is blind=TRUE, which does the same thing as setting an intercept-only model).

Source: https://www.bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#blind-dispersion-estimation

This tripped me up a bit as I was exploring the code, although in hindsight it makes perfect sense: it is mentioned explicitly in several places that the rnaseq pipeline does not take into account any sample metadata, so ~1 is the only possible design to use, and the deseq2 docs clearly recommend using blind=T (the default) for exploratory quality control plots.

Since blind=TRUE is the default, I guess specifying it in the code is a bit redundant, but personally I like explicit code more than implicit.

Cheers!

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github-actions bot commented Aug 29, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 760e83f

+| ✅ 173 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-09-03 14:32:34

pinin4fjords
pinin4fjords requested changes Sep 2, 2024
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Agree with everything except restating defaults in the function calls.

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@pinin4fjords pinin4fjords merged commit 1190e6c into nf-core:dev Sep 3, 2024
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@pinin4fjords pinin4fjords added this to the 3.15.0 milestone Sep 3, 2024
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