Week 3 [July 20th - July 26th]
concise overview of things learned:
- Learned what the batch correction is, and how to build a model matrix for batch correction
- Understanding various quality control/normalization techniques
- Compare before/after each action, and figure out the effectiveness of the normalization, batch correction
- Labeling and plotting the PCA plot, box plot, heatmap
- Convert an object to desired class object and use those to the appropriate function
- How to deal with memory issue when placing/processing datasets
- R, R studio
- Stemaway forum
- Github/Stack overflow/ Google: To get help
- Communicate with my team to solve the problem via Stemaway forum
- Finish deliverables a day before the deadline and compare the results with teammates
- Learned how model matrix works and what format should they have, and made model matrix with the help from Anya
- Successfully contacted with my teammates, and corrected my heatmap with the help of Xuewen - plenty of communication!
- Answered one question on Stemaway forum
list of meetings attended including team events:
- 7/20 team meeting
- 7/23 Office Hour
I wanted to participate in the happy hour, but it was pretty late to me, and I was really tired to stay up till 5 am. I will try to be at the happy hour this week.
goals for upcoming week:
- Manage my task done before the office hours and use OH to get more help
- Communicate with teammates on slack and get to know each other more!
- Try to attend the happy hour!
- Start new deliverables earlier than the last week
- Use slack as a communication tool
detailed statement of tasks done:
It was my first time programming with raw data, and first time using R as a technical tool. So doing the deliverables by myself was pretty challenging, but glad to finish all four deliverables. I used simpleaffy and affyPLM for quality control, and gcrma for normalization tool. I struggled to plot similar to the example ones. My biggest obstacle on this week was the batch correction. I understood the concept of the batch correction, but no idea how to deal with the functions and model matrix. I searched Github, Stack overflow, Googles, and used Stemaway troubleshooting posts. I learned that the ComBat batch uses a single covariant, and the model matrix should be a vector, not the data frame. So I used the ~factor and c(,) to make the desired model matrix. This was my biggest achievement this week. I plotted the data with PCA and heatmaps. I made tons of mistakes and errors doing this week’s deliverables, but happy to finish it with many people’s help.