Self-Assessment 1, Same as April
- An introduction to bioinformatics methods, tools, and different types of data used in bioinformatics analyses
- Introduction to navigating, using, and debugging in RStudio with R
- Introduction to reading and interpreting scientific papers
- RStudio packages
- Additional Resources:
- YouTube tutorials (bioinformatics
- Frontiers in Genetics (paper)
- LinkedIn (downloading latest version of R)
- ggplot2 website
- Conflict resolution: I ran into a few errors while working through the tutorials, I learned that googling the error and using certain phrases could help resolve logic errors in code
- Flexibility and Adaptability: I was not very familiar with RStudio previous to this tutorial, and was not accustomed to its layout or the R syntax. From this tutorial, I gained skills on how to adapt to new situations and learned new skills.
- Self-management: Since the tutorials are self-guided I had to be sure to learn in a way that works best for me. This often meant re-reading the tutorials multiple times and taking my time to make sure that I retained information
- Attention to Detail: R is a very detail-oriented language, the most common error I ran into was confusion over capslock and lowercase. I learned to be a more active reader and picked up on problems better after this module.
- Commitment: This module took me a while, but I stuck with and learned the importance of fulfilling a task, no matter how hard it is. In the end, I learned a lot and grew as an individual.
Three achievement highlights
- Learned how to use ggplot2 to construct volcano plots and boxplots with a given dataset. This allowed me to learn how to work with the R syntax and also allowed me to learn what each component of code meant and how it worked in a visual way.
- I also gained technical and practical knowledge in how to use R and Rstudio and also how to read a research paper to retain the most information possible.
- Additionally, I learned how to troubleshoot code and how to be an effective problem solver when the code from the tutorial didn’t work on my end.
A detailed statement of tasks completed. State each task, hurdles faced if any, and how you solved the hurdle.
- I previously downloaded R Studio, but had not downloaded the latest version of R. Therefore, I looked at a LinkedIn article on how to update R to help me with this task.
- I followed the PDF tutorials for getting familiar with R and creating a new project
- I tried copying down the code from the PDF with the library(Biobase), however, I got the following error message: Error in library(Biobase): there is no package called ‘Biobase.’ I resolved this by googling the error and downloading the package according to the BioConductor web page instructions. This ended up working.
- The tutorial ran smoothly after that, I ran into a minor case error with my variables, but I was able to sort it out.
- Learned about different data types, vectors, variables, factors, matrices, data frames, and lists
- Learned about different functions and how to seek help with functions
- Installed and successfully loaded ggplot2
- Learned how to read .csv files using R, I downloaded the sample data and it worked smoothly
- Data visualization in R: through the tutorial I made a histogram, plots, bar plots, histogram, and boxplot (ran smoothly, but took me a while to adjust to the syntax and figure out what each component of code meant)
- Created an enhanced volcano plot and boxplot using ggplot2
- Looked over textbooks
- Watched the 2020 student StemAway presentation on YouTube for a background in Bioinformatics
- I started reading the Guo paper, but have only read the abstract and part of the introduction and taken notes