- I learned a great deal about the program, its packages, and the overall data processing process. In terms of technical skills, I was able to use the packages to conduct quality control and normalization on the dataset. I also learned how to address issues with the code. Though I did not collaborate with my team as much as I intended to, I still kept up with the discussions and attended nearly all the meetings.
- I was able to create the plots for the deliverables, understand the importance of each processing step and its function, and identify few errors in the code
- I attended all but two meetings: the happy hour and office hours on Thursday
- My goal for this week is to more actively collaborate with my group and not lag behind on the deliverables too much. This past week, I was initially a little behind, and then had to completely restart the entire process, from which I am still working on catching up.
- Completed: creating plots for normalized and raw data
Challenges: Errors in code resulting in incorrect plots, solved by asking questions and referencing other code #bioinformatics-summer2020 #bi-team3-july2020 #quality-control #normalization #arrayqualitymetrics
- I learned about the process of dge analysis, the role each step plays in the pipeline, and how to perform gene filtering and limma analysis. Additionally, from the meetings, I learned about the possible variations in results due to different approaches, and how they are addressed.
- I successfully completed the steps of the deliverables, obtained the volcano plot and heatmap, became more familiar with some of the R packages
- 7/27, 7/28, 7/30, 8/3, 8/4. I could not attend the two meetings on Friday as I had a band camp to attend
- My goal for this week is to attend all the meetings and ask more questions.
- Completed: creating volcano plots and heatmaps for the data
Challenges: Errors in the code and the plots, solved by cross-checking with the group’s data and making necessary changes. Additionally, I had to spend some time understanding the actual process that was taking place, before proceeding with the deliverables. #bioinformatics-summer2020 #bi-team3-july2020 #dge-analysis #limma-analysis #gene-filtering #volcano-plots
- I learned how to use several new functions to perform functional analysis. In addition to the coding, I also learned about the importance of functional analysis and its practical applications.
- Made good progress with the deliverables, familiarized myself with new R packages
- 8/5, 8/7, 8/10
- My goal is to finish the deliverables and get started on the final project
- Challenges: Errors in the code, specifying arguments for the functions - solved by checking online examples and trial and error #bioinformatics-summer2020 #bi-team3-july2020 #functional-analysis #final-project #selfassessment #bioinformatics-pipeline
In this internship I learned a great deal about the steps in creating a bioinformatics pipeline and the significance of each step. I also learned a lot about R coding, which I was completely new to. I learned how to create plots and manipulate data to obtain specific results. I was also introduced to GitHub, which I will explore for myself in the future. In terms of the deliverables, I was able to complete everything through the DGE analysis. Although I started the functional analysis, I was not able to make much progress. Regardless, I still paid attention and understood the importance of each step in the overall pipeline. I did this by attending meetings, reading outside resources, watching videos, etc. Finally, this internship helped me improve my project management skills, and pushed me to keep up with my group and complete the deliverables on time. All in all, this internship was a great experience as it helped me expand my knowledge and skill set in the field of bioinformatics. #bioinformatics-summer2020 #bi-team3-july2020 #dge-analysis #quality-control #bioinformatics-pipeline
Continuation: I faced several challenges during the internship, as I had no prior experience with R and the pipeline process. Most of these challenges were code related. To fix these issues, I had to use external resources, such as R documentation, videos, code examples, etc. Additionally, I spent additional time learning about the importance of each step in the pipeline. I felt like it was more important to understand the concept rather than blindly complete tasks. I want to thank the leads and everyone involved in making the internship a great educational experience. #bioinformatics-summer2020 #bi-team3-july2020 #selfassessment #bioinformatics-pipeline #teamwork
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