DEG Analysis- Meenoti Thakore

DGE Analysis Progress Summary

Group presentation:
https://docs.google.com/presentation/d/1oHrdFy0xB7RqUCjVHbcnGOkWD54uY-TRsthBLQ1j1NA/edit?usp=sharing

Challenges faced:
I thought this week was one of the more challenging weeks. I struggled with the collapseRow() function and also found that the heatmap and volcano plot differed from my group members. We discussed this issue during team meetings and office hours and found that it could have been due to different normalization methods.

Summary of work:

  • Going through annotation and gene filtering to remove under expressed genes
  • Used top table to extract the DEGs by adjusting the p value and plotted the top 50 DEGs in a heatmap, and a volcano plot
  • Wrote the top 100 differentially expressed genes to a file
  • Communicated and worked with subgroup to troubleshoot problems and create our deliverables presentation

Further notes:

  • During this week, I could have managed my time better and used office hours more effectively to get my questions answered.
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