Microarray Pathway Analysis Update: pathway_analysis_microarray_04_qusage_replicate_vignette.Rmd

[cansavvy]

We need the main update items listed on #173 to happen here :

• Have the getting started template material added to it (# 146)
• Update to adhere to the style guide (Contributing guidelines #148)
• Add the dataset added to the S3 bucket. (See https://github.com/AlexsLemonade/refinebio-examples/blob/master/CONTRIBUTING.md#adding-datasets-to-the-s3-bucket)
• Add to the Snakefile and render with snakemake on the Docker container.

• This notebook starts off with some annotation steps, we should link to our annotation gene id microarray notebook for further reference.
• To my knowledge this is the first notebook that will save an RDS file. We should add some more explanation around that. We can borrow sentiments from training-modules/intro-to-R-tidyverse where needed.
• We might want to turn the base boxplot at the end into a ggplot2 boxplot.

Other issues and strategies will likely need updates, but this is what I can see as of now.

[cansavvy]

QuSage notebooks should probably be evaluated as a set #215