Irock194 - Bioinformatics (Level 1) Pathway

[irock194]

Technical:

• I created a metadata file using data from the GEO database.
• I used the Bioconductor package GEOquery to create the metadata file.
• I downloaded multiple packages such as Affy and tkWidgets to read multiple CEL files.
• Learned how to use the merge function to combine multiple data sets.

Soft Skills:

• Debugging and problem solving.
• Read documentations on packages.

Tools:

• R/R Studio
• 7 Zip
• GEO Database

Achievements:

• Download data from the GEO database and create a metadata file inside R Studio.
• Learned how to successfully install packages that are required to read CEL files.
• Learned how to read through the documentation of packages.

Difficulties:

• Using Affy was hard initially because I did not know that the ReadAffy function needed another package to read multiple CEL files.

[irock194]

Week 3 Self-Assessment

Technical:

• Learned how to use multiple control packages such as affyPLM.
• Learned how to normalize a data set and create a heatmap, QC report and a PCA graph with the data set.
• Learned how to directly access information from the GEO database using getGEO.

Soft Skills:

• Debugging and problem solving.
• Collaboration with team members.
• Presentation skills

Tools:

• R, RStudio
• GEO database
• Collaboration tools for communication

Achievements:

• Worked together with Ashlesha to present our deliverables which include data output of affyPLM, RLE and NUSE boxplots, heat maps, and creating PCA graphs.
• Learned how different file formats such as AffyBatch and CEL files.
• Successfully create heatmap graphs and PCA graphs.

Difficulties:

• Was confused on how to access the data from an AffyBatch. Had to research and look up tutorials on how AffyBatch works and how to access the specific data that is needed.
• Used the wrong data set inittialy.
• It was difficult to understand what a PCA graph is.