Here are the issues I faced during the Assignment 2.

Preliminary set up

1. I had to copy some code from A1 to load the normalized data set. I had initially tried to use knit function to load the contents from A1 to A2, but I kept getting errors which I spent multiple hours trying to fix but I made no progress. As a temporary fix, I copied the important code from A1 into A2 and continued for the time being.

Differential Gene Expression

1. I was finding the best factors for the analysis but was unable to decide. So, as a solution, I created a visual using MDS for each factor in the data set and picked the independent variables based on the plots.
2. I had faced some issues during the running of the heat map. When I ran the heat map, I kept getting a weird error. When I searched up the error online, I was told its because I don't have certain permissions (which is typically faced by Mac users). So I used the Online R-studio server hosted by UofT and ran the heat map.
3. I had also realized that I loaded my normalized data set wrong, I had forgotten to set gene names as the row names which caused a lot of issues when I reached the creation of heat map section. It was an easy fix as I just had to add the row names which was one line of code. The hardest part was hunting down the line where the normalization occurred.

Thresholded over-representation analysis

1. I wanted to run G:Profiler query from the markdown file instead of running it on the website but I was not sure what methods to use so I consulted Online R-Documentation for usage of G:Profiler and followed the steps there to complete the query.

Interpretation

Did not have any difficulties in this section

Running on docker

I just used the command below and everything knit properly

docker run --rm -it -v "$(pwd)":/home/rstudio/projects --user rstudio risserlin/bcb420-base-image:winter2024-arm64 /usr/local/bin/R -e "rmarkdown::render('/home/rstudio/projects/A2/A2_JoshiKrutika.Rmd',output_file='/home/rstudio/projects/A2/A2_JoshiKrutika.html')" > processing_output_filename