Assignment 3 - bcb420-2024/Krutika_Joshi GitHub Wiki

Difficulties I faced during A3

Reorganizing the file/Github

  • I realized my file structure was very messy so I reorganized the files but later got an error when I was pushing the changes
  • There were two main errors, I forgot to add the .gitignore which cause large files such as ./Rdata to cause errors
  • There was .DS_Store in A2 which I had deleted in the online git repo but not in my local directory. This caused merge conflicts.
  • Once I added .gitignore, I was able to solve the issue
  • I also used stack over flow to learned how to used rebase to fix the error

Non-thresholded Gene set Enrichment Analysis

  • I forgot to set the run_gsea variable to be false after running it once which cause knitting to take a lot of time. In addition it caused errors while running the heat map since 2 GSEA preRanked files were created. It was an easy fix, just needed to change run_gsea to FALSE. But this error took me quiet some time to figure out.
  • Aside from that, since I had practiced using GSEA from the Journal entry, I knew how to run this section of the lab

Visualize your Gene set Enrichment Analysis in Cytoscape

  • I was initially confused on how I can add the .jar extensions to Cytoscape, but after watching a couple of YouTube videos I figured out we need to click on app section to add the extension
  • Running Cytoscape was simple once I watched lecture videos to follow along

Dark matter

  • I kept getting the following error on my Mac. I checked on multiple websites such as the gitHub support and stack overflow but nothing seemed to solve the problem. As a temporary fix, I used the online UofT R servers to run the heat map and attached a screen shot of it on the assignment.

Error in getFromNamespace(device_info[3], ns = device_info[2])(temp_image) : unable to open /var/folders/9z/zh34x7t13dxgy_1w3pn8zkmw0000gn/T//RtmpgitZkD/.heatmap_body_455ed3f7aff9d8d0c92266c9de67e33f_1_13325d0e4c56.png

Knitting

  • I had used the child method to load pervious assignments into A3:

```{r child = '../A2/A2_JoshiKrutika.Rmd'} ```

  • When knitting I got an error saying "setup" already exists. I later realized the error stemmed from called two r-chunks the same on A2 and A3(it was when I was loading the packages).