Last updated: 2018-08-20

workflowr checks: (Click a bullet for more information)

• ✖ R Markdown file: uncommitted changes

  The R Markdown file has unstaged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

• ✔ Repository version: e920e39

  Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.
  
  Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:

  
  Ignored files:
      Ignored:    .Rhistory
      Ignored:    .Rproj.user/
  
  Untracked files:
      Untracked:  code/counts_per_sample.txt
      Untracked:  code/table-s1.txt
      Untracked:  docs/figure/linear-models.Rmd/
  
  Unstaged changes:
      Modified:   analysis/ch01.Rmd
      Modified:   analysis/index.Rmd
      Modified:   analysis/linear-models.Rmd
  
  Staged changes:
      New:        analysis/linear-models.Rmd
  
  

  Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

Expand here to see past versions:

File	Version	Author	Date	Message
Rmd	31cf81a	John Blischak	2018-08-20	Remove data files associated with unused lessons.
html	f2c0198	John Blischak	2018-08-09	Build site.
Rmd	6893542	John Blischak	2018-08-09	Organize analysis of batch effects in TB data.
html	eafed69	John Blischak	2018-08-09	Build site.
Rmd	75f3f79	John Blischak	2018-08-09	Organize analysis of pre-processing raw Arabidopsis data.
html	5cf7b98	John Blischak	2018-08-08	Build site.
Rmd	457f59b	John Blischak	2018-08-08	Organize analysis of Arabidopsis used in slides to demo 2x2 factorial study.
html	651524a	John Blischak	2018-08-08	Build site.
Rmd	d2c5c34	John Blischak	2018-08-08	Organize analysis of leukemiasEset used in slides to demo study with 3 groups.
html	ad13021	John Blischak	2018-08-02	Build site.
Rmd	010a04c	John Blischak	2018-08-02	Convert vdx analysis to Rmd and increase font size in figs.
html	9b58c25	John Blischak	2018-05-23	Build site.
html	79a1ea4	John Blischak	2018-05-23	Build site.
Rmd	3e36241	John Blischak	2018-05-23	Update to 1.0
html	3e36241	John Blischak	2018-05-23	Update to 1.0
html	6209669	John Blischak	2018-02-16	Build site.
Rmd	221239f	John Blischak	2018-02-10	Add scaffolding for ch01 from index.
html	cf73f46	John Blischak	2018-01-26	Build site.
Rmd	d61faa9	John Blischak	2018-01-26	Add Chapter 02 analysis.
html	3bcf168	John Blischak	2018-01-12	Build site.
Rmd	20cdf3d	John Blischak	2018-01-12	Fix typo in links.
Rmd	6395f07	John Blischak	2018-01-11	Start organizing Ch 03
html	17de7de	John Blischak	2018-01-11	Build site.
Rmd	93052d7	John Blischak	2018-01-11	Apply workflowr infrastructure. Committed files manually.

---

Lesson material for differential expression analysis with limma.

Case studies:

• 2 groups: Breast Cancer VDX
• 3 groups: leukemiasEset: ALL v. AML v. CML
• 2x2 factorial: Effect of low temperature on Arabidopsis
• Pre-processing features (genes): Raw Arabidopsis data
• Accounting for technical batch effects: Response to infection with Mycobacterium tuberculosis

Supplement:

• Understanding linear models

• Chapter 1

---

This reproducible R Markdown analysis was created with workflowr 1.1.1

---