I’ve been trying to identify diferentially expressed proteins in Rhonda’s oyster data, however there has been significant difficulty finding a way to compare the different treatments or days. Initially I would take the differences between the proteins however this did not consider the majority of proteins in the ABACUS data which means I could be missing important enriched genes. Furthermore, finding the differences between two days was simple when looking at the differences, but impossible when comparing all 13 days with each treatment.
Working with Sean, we tried a PCA plot and K means clustering however neither worked effectively. Yaamini is using MSstats to analyze her Skyline data. I am not sure if ABACUS data can be analyzed using MSstats but I know MSstats can analyze DDA so I am going to look into it further.
I helped Yaamini label some tubes for her and Laura’s DNR a little today as well!