Ena Haseljic-Bioinformatics Pathway-Self-Assessment

concise overview of things learned

Technical area: learned about normalization, and how it affects analysis of biological data. Learned how to create a file using write.csv(). Learned about quality control methods.

Tools: creating ggplots and heatmaps in R

Soft skills: collaboration with teammates about deliverables.

three achievement highlights

  1. Learned how to create and interpret heatmaps.

  2. Created account on GitHub and Slack and learned how to use them.

  3. I was able to troubleshoot most of problems I encountered in R.

list of meetings attended including social team events

I attended webinar, Happy Hour and overall group meetings.

goals for the upcoming week

1)Better time management with deliverables.

  1. Attending office hours.

  2. Learn how to submit code in GitHub.

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

1)Did Deliverable 1- did not have any problems with quality control and finding outliers.

  1. Was able to finish normalization (gcrma()) and creating boxplots.

3)Was able to generate CSV file containing batch data.

  1. Was able to create heatmaps.

  2. Had difficulties with creating ggplots as I kept getting message that vector of a certain size cannot be allocated. But even after using memory.size() the error could not have been fixed and I was not able to make plots.

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concise overview of things learned

Technical area: learned about techniques used in differential gene analysis.

Tools: creating heatplots and volcano plots. Using EnhancedVolcano, WGCNA, Limma and other packages to analyze differentially expressed genes.

Soft skills: collaboration with teammates about this week’s deliverables.

three achievement highlights

  1. Learned how to create volcanos.
  2. Learned basic functions on GitHub
  3. Attended all overall group meetings and group discussion meeting.

list of meetings attended including social team events

I attended overall group meetings and Group Discussion meeting.

goals for the upcoming week

1)Start early on with deliverables in case my computer crashes again.

  1. Attend Happy Hours.

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

We used packages to do analysis. I was not able to do collapseRows() in order to get rid of duplicates. We used different method instead. We generated table with 100 differently expressed genes and plotted a heatmap. I was unable to generate Volcano plot due to having duplicates, but after work with my team, I was able to solve the problem.

concise overview of things learned

Technical area: learned about functional analysis,global enrichment analysis,gsea analysis (how to interpret it)
Tools: creating dotplots,using Slack for the first time, learned about using names(), gene-concept maps, gseaplot(),survival analysis.

Soft skills: collaboration with teammates about deliverables,attending few coding sessions we organized.

three achievement highlights

  1. Used Slack.
  2. Using “Kyoto Encyclopedia of Genes and Genomes” for the first time.
  3. I was able to understand and do most parts of deliverables.

list of meetings attended including social team events

I attended overall group meetings (Diversity Discussion as well).

goals for the upcoming week

  1. Finishing a final project and understanding genes involved in Parkinson’s Disease.

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

  1. Used results from limma analysis to create a gene vector. Used enrichGO and KEGG analysis by using enrichKEGG and created a barplot and dotplot.
    2)Performed GSEA analysis using GSEA(). Created cnetplots. I faced problems with gsea(), but was able to solve the problem with teammates.

[quote=“Ena_Haseljic, post:1, topic:5297, full:true”]
concise overview of things learned
This assessment is regarding my final project.
Technical area: reviewed all the steps we utilized during the internship, reviewed how to interpret heatmaps. Learned how to make batch data and understand Series Matrix File.

Tools:improved my skills on creating ggplots and heatmaps in R. I had problems with visualization at the beginning.

Soft skills: got better at time management (was able to finish project on time), resolving problems with RStudio as it was slowing down my computer.

three achievement highlights

  1. Learned how to create batch data.
    2.My teammates and I were checking on each other about progress of our projects.
  2. I was able to troubleshoot most of problems I encountered in R.

list of meetings attended including social team events

I attended overall group meetings.

goals for the upcoming week

1)Attend final meeting.
2) Stay in contact with teammates.

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

1)Did quality control, DGE analysis and functional analysis.
2. Was able to finish normalization (gcrma()) and creating boxplots, was able to do DGE analysis without problems.

3)The only problem I encountered was making volcano plots as I did not label axis correctly.
4.) Was not able to make cnetplots as I did not set the right value for upregulated and downregulated genes.
5) was able to do gsea analysis, kegg analysis and enrichGO()

concise overview of things learned
This self-assessment is about my experience in the internship.

Technical area: I had only basic knowledge prior to the internship. I knew how to make plots and do basic statistical analysis. Now, I know how to manipulate different data and analyze them in R. I know how to make different kind of plots(cnetplot, heatmap, ggplot,etc.) I learned about DGE and functional analysis.
Tools: using R to make plots, process data and visualize results.

Soft skills: collaboration with teammates about deliverables, meeting many people in my group and learning a lot about and from them.

three achievement highlights

  1. Learned how to create and interpret different types of plots.
  2. Created account on GitHub and Slack and learned how to use them.
  3. Made new friends.
    list of meetings attended including social team events

I attended most of group meetings, first Happy Hours and few office hours.

goals for the next internship

1)Better time management with deliverables.
2)Attend more social events.

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

I was able to do most of deliverables by myself. Biggest challenge was using R as it was slowing my computer and I had to invest a lot of time to finish deliverables.