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carpentries-incubator / bioc-rnaseq

Analysis and Interpretation of Bulk RNA-Seq Data using Bioconductor
https://carpentries-incubator.github.io/bioc-rnaseq
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De analysis #56

Closed almutlue closed 1 year ago

almutlue commented 1 year ago

Add descriptions, further explanations and challenges to the DE section following the DESeq2 workflow.

There are a few points that might be good to double-check:

  1. I used function calls without package name ( DESeq() instead of DESeq2::DESeq()) as done in the explanatory data analysis section.
  2. I needed to install but not explicitly load the apeglm package for DESeq2::lfcShrink() to work.
  3. Filter lowly expressed genes via indepent_filtering() is performed by default, but was explicitly mentioned in the session outine. I added a challenge about it to show the effect, but I'm not sure that was the expected intention?
github-actions[bot] commented 1 year ago

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:

Rendered Changes

:mag: Inspect the changes: https://github.com/carpentries-incubator/bioc-rnaseq/compare/md-outputs..md-outputs-PR-56

The following changes were observed in the rendered markdown documents:

 05-differential-expression.md                      | 314 +++++++++++++++++----
 data/GSE96870_se.rds                               | Bin 2411112 -> 2411113 bytes
 ...xpression-rendered-unnamed-chunk-16-1.png (new) | Bin 0 -> 29720 bytes
 ...xpression-rendered-unnamed-chunk-19-1.png (new) | Bin 0 -> 20318 bytes
 ...ntial-expression-rendered-unnamed-chunk-8-1.png | Bin 20316 -> 53602 bytes
 md5sum.txt                                         |   2 +-
 6 files changed, 266 insertions(+), 50 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 2023-07-19 11:48:48 +0000