Anirudh Sriram - Bioinformatics - Self-Assesment

QC
Overview of things learned:

  • Technical : I learned how to Perform Normalization and Batch Correction using R. I also learned how to plot the results of these functions, in order to analyze them, in the form of RLE, NUSE, PCA, and Heatmap plots.

  • Tools : R, Slack, and Stem-Away forums

  • Soft Skills : How to communicate with people in different time zones.

Three achievement highlights:

  • I was able to successfully complete quality control and plot data using the affyPLM package in the form of RLE and NUSE Plots

  • I was able to plot results from before and after batch correction in PCA Plots in order to visualize the data

  • Using different forms of quality control and visualization, my team and I were able to identify possible outliers in the data set.

List of meetings attended:

  • I attended all of the Monday and Tuesday team meetings.

Goals for the upcoming week:

  • Connect more with my team

  • Learn how to use R in order to do Differential Gene analysis

Detailed statement of tasks done - specifically challenges and how those challenges were overcome

  • I Finished all 4 deliverables, but faced challenges while attempting to label PCA Plots

DGE Analysis
Overview of things learned:

  • Technical : Learned how to perform Annotation, gene filtering, and Limma analysis
  • Tools : R, Slack, and Stem-Away forums
  • Soft Skills : Learned how to work with teammates in order to come up with a hypothesis

Three achievement highlights:

  • I was able to successfully use the select() function in order to create a matrix containing a column of Probe ID’s, and their respective gene symbols

  • I was able to successfully filter out the genes that were in the bottom 2 percent of the data set

  • I was the task lead for this week

List of meetings attended:

  • I attended all of the Monday and Tuesday team meetings.

Goals for the upcoming week:

  • Attend more meetings
  • Learn how to use R in order to do the next set of deliverables.

Detailed statement of tasks done - specifically challenges and how those challenges were overcome

  • I Finished all of the deliverables with no major issues. All of my questions were answered in the forums.

Functional Analysis
Overview of things learned:

  • Technical : Learned how to perform Functional analysis, Survival analysis, and transcriptional factor analysis
  • Tools : R, Slack, and Stem-Away forums
  • Soft Skills : Learned how to work with teammates through slack communication

Three achievement highlights:

  • I was able to plot barplots using enrichGo() and groupGo()
  • I was able to graph a cnet plot through the use of transcriptional factor analysis
  • I was able to complete survival analysis using the GEPIA website

List of meetings attended:

  • I attended all of the Team meetings.

Goals for the upcoming week:

  • Attend more meetings
  • Learn how to use R in order to complete the final project

Detailed statement of tasks done - specifically challenges and how those challenges were overcome

  • I Finished all of the deliverables with no major issues. All of my questions were answered by my teammates

Final Presentation
Overview of Things Learned:

  • Technical : Increased understanding of Functional analysis
  • Tools : RStudio, Stem-Away Forums, Slack, GitHub
  • Soft Skills - Learned how to complete the deliverables independently without the help of a team

Achievement Highlights:

1.Successfully completed all of the deliverables
2. Successfully designed and completed a pipeline
3. Successfully troubleshot errors.

List of meetings attended:

  • team meetings: 8/14, 8/17

Goals for upcoming week

  • Present final presentation

Tasks Completed

*Finished all deliverables from the final presentation.