WEEK 3 SELF ASSESSMENT
I got better understanding of doing quality control analysis of the dataset using SimpleAffy and arrayQualityMetrics packages. In addition to that, I interpreted the QC results to detect the outliers. I learned to normalize the data using rma normalization method, and remove the variability arising due to batch effect using sva package. I was able to make PCA plots, and heatmaps for both normalized and batch corrected data. Through this week’s learning process, I realized the importance of having patience, since the arrayQualityMetrics package was taking too much time to run. At the beginning of this week, I was so impatient to get QC results and proceed for batch correction and plots, that I did not give time to the program to run, and rather closed it down without waiting for the output. I wasted 2-3 days in this whole process. Since time was running out, I had no other option but to patiently wait for the program to run, which ultimately gave me my ‘index.html’ (although it took me few hours). I also learned to coordinate work with other team members. Communicating with my colleagues was bit challenging due to the huge time difference (12.5h), but I managed it well. I’m glad about the fact that we were able to put together all the deliverables and a decent presentation, in time, all because of effective teamwork. Another challenge I faced was to allocate large sized vectors, and I figured out a way to that too (by increasing the memory limit)!
My three achievements for this week are:
One, I learned to make and interpret different plots like QC plot, boxplot for array intensities, NUSE and RLE plots, and heatmaps based on pearson correlation to detect outliers and check data quality. Two, I was able to perform principal component analysis, and three, I effectively communicated with my fellow group members (using slack and Gsuite account), and also cleared my doubts by communicating with other team members and leads.
I attended all team meetings and office hours, except the BI happy hour, as it was late in the night here. For week 4, I have volunteered as the task lead, and my approach will be to make sure everything is conducted smoothly and tasks are completed in time. Also, my goal for this week is to work in a more systematic manner in order to complete my individual tasks, and to manage my time efficiently.