Quality Control and Data Visualization - Croix Mikofsky

Progress Summary- Quality Control

Group presentation:
https://docs.google.com/presentation/d/1xJwxMirH6yh5GPZwPgYowe8xyOH2o0PFu6iKbKJ-Tzk/edit?usp=sharing

Challenges faced:
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. (I would come to realize the next week that there indeed was an error with the ordering of my raw datasets in my affyBatch object)

Summary of work:
Technical - Using the various R Studio tools to prepare data for DE analysis
QC (simpleaffy, affyQCReport), Normalization (RMA), also PCA
Tools - RStudio, Troubleshooting (stackoverflow, R website, etc), slack, google meet, stem away forum
Soft Skills - Networking, intra-team communication.

Further notes:
Nothing much. In the future it would be nice to investigate different quality control methods, especially ones that would be readable for large datasets. ( cough cough I’m looking at you, affyQCReport)

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