Overview of things learned:
Technical - Using the various R Studio tools to prepare data for DE analysis
Tools - RStudio, Troubleshooting (stackoverflow, R website, etc), slack, google meet, stem away forum
Soft Skills Networking, intra-team communication.
Three achievement highlights:
1.) Successfully finding and working out an error in my code with the help of office hours
2.) Met with my group regularly, and completed assignments in a timely manner
3.) Learned valuable bug finding strategies which I’m sure will come in handy later
List of meetings attended including social team events:
Monday meeting, Tuesday bio webinar, Wednesday group meeting, Thursday office hours, Friday Happy Hour
Goals for the upcoming week:
Flesh out my linkedin profile
Work more closely with my group to complete our deliverables
Hone github skills and get practice with version control.
Relate my findings with the paper for a better understanding of the biology aspect
Detailed statement of tasks done:
Quality control using AffyQCReport
Normalization using RMA
Batch correction using ComBat()
PCA plotting ( prcomp() then ggplot() )
Challenges and how those challenges were overcome:
I had a dimensions problem with my affy object which prevented me from conducting a batch correction. I went to office hours and tried many things to troubleshoot, and in the end we were successful in finding the (tiny) error.
I was initially unsure as to whether or not my PCA plots were correct because they didn’t match the document well, but after meeting with my group and talking it over, I couldn’t find any issues with my process or data so it was resolved as a non-issue.
No real non-technical issues. My team was quite responsive and helpful for the most part.
also, P.S. thanks @sona I kind of borrowed your formatting for the self assessment. I found yours very clear and easy to read.