Module 4
Technical area:
- Collaborating in testing the Shiny app
- Removing outliers from datasets
- Getting the annotations from Databases
- Removing duplicated Probe IDs and the genes which don’t have any corresponding Probe IDs
- Selecting a representative row from the rows with duplicated Symbols
- Filtering out genes below the 2nd percentile of the expression distribution of the dataset
- Differential expression analysis by Limma package
- Plotting a volcano plot in which the differentially expressed genes are identified
- Plotting a Heatmap with expression values of the top 50 most significant genes
Soft skills:
- Presenting a presentation on teaching the codes in detail to the others
- Troubleshooting the Errors that I was being got from implementing the codes
Tools:
- hgu133plus2.db
- limma package
- EnhancedVolcano package
Achievements:
- Obtaining the list of differentially expressed genes of Colorectal cancer
- Plotting Volcano plot and heatmap on the expression values of differentially expressed genes
- Preparing a presentation on module 4
Hurdles:
I had some problems in removing duplicated Prob IDs, removing genes that were not mapped to any symbols, and selecting a representative for rows with duplicated Symbols. That was fixed by searching for different tutorials and different sites on the net.