Things learned:
Technical area: Learned how to use Python, brushed up on and improved my capabilities with R, and gained an understanding of the genetics and different RNAs involved with the paper.
Tools: Learned how to use Python and Asana, how to better use R, and learned the basics using GEO2R
Soft Skills: Learning to navigate the Stem-away website and Slack as well as the communication skills involved in attending meetings and working to understand the paper with people in breakout rooms.
Achievements:
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Improved my skills in R and Python and completed the exercises for them.
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Gained skills in communicating and remaining organized using Slack, the Stem-Away forum, Google Meet, and Zoom.
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Read through and comprehended the paper and analyzed its figures
Meetings/trainings attended:
6/1 Webinar, Team 3 Email Set Up Meeting, 6/2 R Training, 6/3 Bioinformatics webinar, 6/5 R Training, 6/6 Python Training, 6/9 Python Training, 6/10 Technical Training Webinar, 6/10 Leadership webinar, 6/11 Gene Team Meeting, 6/12 R Training, 6/12 Happy Hour, 6/15 Gene Team meeting, 6/16 Asana Training
Goals for upcoming week:
Read the paper again and make sure I completely understand the figures, as well as working with my group to do the expected quality control work on the data.
Completed tasks:
• Became more proficient with R and especially using it to visualize data. I found the information supplied by R on its methods sufficient to overcome any difficulties implementing them.
• Learned the basics of Python and about the packages in python that we will be using.
• Read the research paper and analyzed its figures with the help of the sessions discussing the figures and using the internet to look up terms and the theory behind certain types of plots.
Things learned:
Technical area: Learned how to use R packages to normalize, analyze, and plot data.
Tools: Learned about and used affyPLM, mas5, prcomps, and asana
Soft Skills: scheduling meetings and communicating with my group in those meetings and over slack.
Achievements:
- Learned how to use R packages relevant to normalizing data, examining RLE and NUSE values, and making PCA plots
- Completed with my group the deliverables for this week
- Communicated and met with my team over Zoom and slack in order to complete the deliverables
Meetings/trainings attended:
6/15 Gene Team Meeting, 6/16 Asana Training, 6/17 Technical Training Webinar, 6/18 Gene Team Meeting, 6/22 Gene Team Meeting
Goals for upcoming week:
Complete the deliverables for Friday and create a presentation for Thursday.
Completed tasks:
Used affyPLM, mas5, prcomps, and other R functions to normalize the data create histograms and boxplots for the RLE and NUSE values, and to create PCA plots. Any issues I had with R were handled by closer examination of either the instructions supplied by the leads or R’s documentation about the functions. We also had some issues understanding the deliverables, which were resolved by reaching out to the leads
Things learned:
Technical area: Learned to create heat maps and volcano plots of genomic data in R and use the limma package
Tools: Learned to use GitHub and the limma and pheatmap packages
Soft Skills: The communication and organization skills used to work in meetings with my group and group 1 to analyze data and work together to create a presentation.
Achievements:
- Completed the deliverables for week 4
- Worked alongside my group and group 4 to create and give a presentation on the week 3 deliverables
- Improved abilities annotating and visualizing expression data in R.
Meetings/trainings attended:
6/24 Fireside Chat, 6/24 Group 1 and 4 Presentation Meeting, 6/24 GitHub Training, 6/25 Bioinformatics Webinar, 6/25 Gene team meeting, 6/26 R training, 6/26 Groups 1 and 4 Meeting, 6/29 Gene Team Meeting, 6/30 Python Office Hours,
Goals for upcoming week:
Present on the week 4 results and complete the week 5 deliverables.
Completed tasks:
• Successfully annotated the data, filtered it based on centile, analyzed it with limma to create a table of the top differentially expressed genes, and created a volcano plot. I had difficulties with several parts of this which were dealt with using the information on the Stem-Away forum, Yves R training video, and help from my group
• Communicated on slack and in a zoom meeting with my group to work together to put together the week 4 deliverables
• Worked with group 1 to create a presentation comparing the week 3 results of both groups.