Module 1
Overview:
Technical Area:
- R programming (reviewing visualization, coding, and debugging on RStudio)
- Process of reading and understanding research papers, highlighting key points and evaluating results
- Getting better informed about Bioinformatics
Tools:
Soft Skills:
- Effectively navigating through the STEM-AWAY website
- Using things I previously learned in an efficient manner
Achievement Highlights
- Successfully downloaded RStudio and got it to run. I had to download RStudio again because I got a new computer. Nevertheless, because I had already done it once before, the process was smooth.
- Revisited the basic understanding of how to display visuals and how to overall code on R.
- Practiced reading research paper on a topic of my choice
Difficulties during Tasks
- Figuring out the internship and where all the information was located was a challenge.
- Reading the research paper on lung cancer for our project was also challenging because there were many complex terms. Luckily, the following kick off meeting helped clear some of the confusion. I think I still have a lot to work when it comes to reading research papers though.
Module 2
Overview:
Technical Area:
- Practicing steps I learned previously to efficiently navigate different resources
- Exploring the ins and outs of GEO database
- Familiarizing myself with raw datasets and matrix datasets
- Extracting metadata into Excel
Tools:
- GEO Database
- RStudio
- STEM-Away
Soft Skills:
- Organizing my directory by modules to make navigation easier
- Using things I previously learned in an efficient manner
- Improving involvement through active engagement, paying attention, and trying to make sense of things in my head (giving honest effort).
Achievement Highlights
- Successfully downloaded the correct expression data from GEO
- Being able to navigate and understand the matrix format a bit better than before
- Learning how to change the orientation of information from horizontal to vertical in Excel. As well as swiftly gathering required data without being confused or overwhelmed.
Difficulties during Tasks
- Because I was disconnected with my internship team, I was unsure if I had to do a self-assessment. After inquiring, I found out that I was missing a big task.
- I had trouble unzipping my datasets because I lacked an application that would unzip files properly. I also accidentally clicked on an option that would open all gz. files as a PDF. I got all of this resolved with assistance from my dad.
- I remember being confused with batches in the pathway and I encountered the same issue here. After some digging, I found out that batches were not necessary when using one dataset.
Module 3
Overview:
Technical Area:
- Background correcting and normalizing data
- Using R to conduct several quality controls and data visualizations
- Analyzing plots to identify outliers
Tools:
- RStudio/R
- GitHub
- Excel
- Slack
Soft Skills:
- Applying knowledge gained from pathway into the internship
- Following instructions and looking at resources for more insights and extra help
- Organizing files and code to improve efficiency
Achievement Highlights
- Being able to follow the module and work through the code without struggling
- Understanding the plots and visualizations and their purpose and results better than before
- Officially joining the internship group after realizing that I was not fully involved in it
Difficulties during Tasks
- I figured out that I was not part of the private internship channels which cause a lot of disturbances in my workflow and confidence. It was very overwhelming to navigate Slack and other platforms. In addition to above, my @mentorchains.com email was not working, so I reached out for help from Kelley, Ivan, Debaleena, and Sarah and got it resolved.
- The QCReport function was giving me an error saying that it didn’t exist. I checked the documentation and it seemed that there was no error in my code. After some time, I figured out that I forgot to install the affyQCReport.
- The vector size for both QCReport and arrayQualityMetrics were too large which introduced me to a new function, memory.limit(), that enlarged the memory size.
Goals for Module 4
- I hope that I can work as well as I did in module 3 (without encountering major issues)
- I also cannot wait to collaborate with my team