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)
I added these extras to episode 4 at the BioC2023 workshop and they should be added in:
limma::plotDensities()Glimma:glimmaMDS()