Progress Summary- Quality Control
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.
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)