Week 10 Blog Post

Hi everyone! Today will be another short post as I am slowly reaching the end of my project and preparing to collect and analyze my results.

This week was mostly focused on labeling the graph that compared the IPF clusters with the Normal sample clusters to potentially help draw comparisons between the cell types involved. While this was simple (and I over complicated the process) I did run into a strange problem which I haven’t been able to understand the cause of. Currently, I have 16 clusters however a few days ago I ran my code and I got 17 clusters despite not changing a line. Then R ended up restarting and I had to re-run all my code from the beginning (which takes hours as there is a lot of data processing and clustering which takes time) and I somehow got 16 clusters again. I looked over my code several times to see if there was something I changed or something that looked right however I couldn’t find anything. 

Another step I worked on was generating upregulated and downregulated genes for each cluster. This was pretty simple as all I had to do was filter through the genes that had a positive logFc value (upregulated) or a negative logFc value (downregulated) and made separate csv files for each. After looking through I have several 1000 for some so I need to see if I can try to filter them further or find a way to prioritize a few of them.

As I am reaching the end of my project my next step is to put all the results I got (including the Bulk RNA) and analyze each graph to form conclusions about my research topic and question. 

Thank you so much for reading!