Richard's Edits

[richard-cassidy]

No description provided.

[rwedan]

Helpful annotations. I also had to install some packages, but I am using desktop so I am not sure if my install code would be helpful for anyone else.
I agree with removing the font, even widening the plot did not make the names readable, and the labels were not helpful. GSM604380 was the only label for the one sample that had mutations in IDH and TET2.

Per rubric:

1. Does the code run? Yes. It runs after I add the code "BiocManager::install("GEOquery") to the first chunk
2. Is the logic in the code sound and properly explained? Tags add explanation to most/all lines. Easy to follow, changes were well explained and beneficial.
   3)Does the code and accompanying text address relevant items such as labeling, comparing, and evaluating each library prep method? Yes. Some lines I also do not know what specifically they are executing, (ie ' load_all("./") ')
   4)Does the analysis (code + writeup) provide a foundation for drawing conclusions about the underlying question ("what affects my results?")? Yes. Scientific conclusions and code critiques written at the bottom demonstrate reasoning and ability to draw conclusions.
3. Are all reviewer questions addressed in a satisfactory manner? My only questions would be what packages did you need to install, and if we maybe had to install the same 'GEOquery' package, in which case that could be added as a line for everyone.

[Christina-Straham]

Richard,
You added a lot of great comments. It helped me understand the purpose of some of the codes (for example, lines 67-74)

Does the code run? Once I added the limma and GEOquery packages
Is the logic in the code sound and properly explained? Richard rationalized most of them out so I think yes.
Does the code and accompanying text address relevant items such as labeling, comparing, and evaluating each library prep method? Yes.
Does the analysis (code + writeup) provide a foundation for drawing conclusions about the underlying question ("what affects my results?")? Richard answered all the necessary questions embedded in the code and summarized his critiques.
Are all reviewer questions addressed in a satisfactory manner? Yes.

[PAMatusiak]

Richard, I want to start by thanking you for your great annotations. Like in the case of Riley and Christina, your annotations were helpful in my ability to review Tim's code and to think critically about the conclusions made by the authors of the original paper.

As far as logic goes, you did a great job at breaking down each step into digestible bites. Your added text was very clarifying. I also appreciated that you informed your audience when you did not need specific code or when you were unsure as to why a certain chunk was utilized in the initial code provided by Tim.

As far as running your code goes: I was successfully able to take your new and improved code and run it in my local Rstudio. Nice work!

Finally, I really appreciated how you had your code critiques and science critiques at the end of your code - so much so that I used a similar format in my pull request! Thank you for the inspiration!

[Goralsth]

pulled Richards code down into R and it runs. Good job

[SI18]

Richard, I looked at your review after completing mine, and it appeared to be complementary to my analysis. Great job on critiques and comments, the code runs well. I did not really dive into scientific aspect and looking at it again, I fully agree with your comments!