Xuewen Geng-Bioinformatics-Self Assessment

Week2-3
In terms of content, please address these points:

  • concise overview of things learned - break it up into technical area, tools, and soft skills
    Technical Area: Learned about how gcrma operate compare to arms.
    Tools: R studio, varies packages
    Soft skills: Communicating with people from different timezone

  • three achievement highlights
    Found out how to plot pca
    Found out how to do batch correction
    Found out how to do heatmap

  • list of meetings attended including social team events
    Just Monday and Tuesday meetings

  • goals for the upcoming week
    Communicate with teammate more
    Attend more meetings

  • detailed statement of tasks done - specifically challenges and how those challenges were overcome
    Four deliverables.
    I really have problems doing pca plots, first not sure about if I should add sdev to calculate a percentage for the plot, second I’m not sure how to do the before normalization plot, latter found out I can use exprs() on the raw dataset.

Week4
In terms of content, please address these points:

  • concise overview of things learned - break it up into technical area, tools, and soft skills
    Technical Area: Learned about how to do limma analysis and gene filtering and the concept behind those methods.
    Tools: R studio, varies packages
    Soft skills: Select genes that are significant, Make hypothesis for next weeks.
  • three achievement highlights
    Found out how to plot volcano plot
    Found out how to do gene filtering
    Found out how to do limma analysis
  • list of meetings attended including social team events
    Just Tuesday meetings
  • goals for the upcoming week
    Being a Task lead
    Attend more meetings
  • detailed statement of tasks done - specifically challenges and how those challenges were overcome
    Three deliverables.
    I have problems in get the CollapseRows() and topTable() work. And keeping track of my variables.

Week5
In terms of content, please address these points:

  • concise overview of things learned - break it up into technical area, tools, and soft skills
    Technical Area: Learned about how to do enrichment analysis and plot appropriate graphs for them. And do analysis according to the results.
    Tools: R studio, varies packages
    Soft skills: Analysis if our hypothesis from last week is appropriate. Revise our thesis through our experiment.
  • three achievement highlights
    Learn how to do GSEA()
    Learn how to use enriched()
    Learn how to use EnrichGo()
  • list of meetings attended including social team events
    Just Tuesday meetings
  • goals for the upcoming week
    Individual Presentation
  • detailed statement of tasks done - specifically challenges and how those challenges were overcome
    All deliverables.

Week7 Final week
In terms of content, please address these points:

  • concise overview of things learned - break it up into technical area, tools, and soft skills
    Technical Area: Learned about how to do enrichment analysis and plot appropriate graphs for them. And do analysis according to the results.
    Tools: R studio, varies packages
    Soft skills: Do individual presentation about a small project. Organize everything
  • three achievement highlights
    • Learn to interpret all the graphs generated from R
    • Learn to explain why each step in the pipeline is important
    • Learn to collaborate with other three people for a bioinformatic project
  • list of meetings attended including social team events
    Final Presentation
  • goals for the upcoming week
    Finished!
  • detailed statement of tasks done -
    A small study that based on geneset GEO22598
    All deliverables.
    Small presentation by myself