fix output errors, add details to DE model and contrast usage

[almutlue]

More changes related to the DE analysis section:

• added references to section about design matrices
• load apeglm to remove the error from the deployment
• added more details and examples on how the GLM is fitted
• added more details about how to specify contrast and how they relate to the design matrix and formular

[github-actions[bot]]

Thank you!

Thank you for your pull request :smiley:

:robot: This automated message can help you check the rendered files in your submission for clarity. If you have any questions, please feel free to open an issue in {sandpaper}.

If you have files that automatically render output (e.g. R Markdown), then you should check for the following:

• :dart: correct output
• :framed_picture: correct figures
• :question: new warnings
• :bangbang: new errors

Rendered Changes

:mag: Inspect the changes: https://github.com/carpentries-incubator/bioc-rnaseq/compare/md-outputs..md-outputs-PR-62

The following changes were observed in the rendered markdown documents:

 01-intro-to-rnaseq.md                              |   4 --
 05-differential-expression.md                      |  59 ++++++++++-----------
 ...xpression-rendered-unnamed-chunk-17-1.png (new) | Bin 0 -> 28464 bytes
 ...tial-expression-rendered-unnamed-chunk-19-1.png | Bin 20399 -> 20324 bytes
 index.md                                           |   5 +-
 md5sum.txt                                         |   8 +--
 setup.md                                           |   2 +-
 7 files changed, 35 insertions(+), 43 deletions(-)

What does this mean?

If you have source files that require output and figures to be generated (e.g. R Markdown), then it is important to make sure the generated figures and output are reproducible. This output provides a way for you to inspect the output in a diff-friendly manner so that it's easy to see the changes that occur due to new software versions or randomisation.

:stopwatch: Updated at 2023-07-20 09:07:11 +0000