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Extras to add to episode 4 #72

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jdrnevich opened this issue Aug 2, 2023 · 0 comments
Open
5 tasks

Extras to add to episode 4 #72

jdrnevich opened this issue Aug 2, 2023 · 0 comments
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help wanted Looking for Contributors type:enhancement Propose enhancement to the lesson

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@jdrnevich
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I added these extras to episode 4 at the BioC2023 workshop and they should be added in:

  • ggsave() for plots
  • distributions of expression values ala limma::plotDensities()
  • interactive MDS clustering ala Glimma:glimmaMDS()
  • Challenge question showing examples of PCA/MDS showing outliers, batch effects, other problems and asking them to evaluate
  • Section on what to do if you have outliers or batch effects. If remove outlier, say to re-do all step from beginning (e.g. any gene filtering, scale factors will change slightly)
@jdrnevich jdrnevich added help wanted Looking for Contributors type:enhancement Propose enhancement to the lesson labels Aug 2, 2023
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