Week 7 Assignment

[jonathanfischer97]

Grading Assessment for Daniel Mendoza-Sanchez

R Script Components

1. Data Loading and DESeq2 Object (1 point)

Score: 1/1

2. VST and PCA Implementation (1 point)

Score: 1/1

3. PCA Interpretation (1 point)

Score: 0.5/1 Feedback:

• PC2 interpretation too vague - needs to specify what gene expression patterns are being seen

4. Differential Expression Analysis (1 point)

Score: 1/1

5. Sex DE Results (1 point)

Score: 1/1

6. Sex DE Interpretation (1 point)

Score: 1/1

7. Death Classification Analysis (1 point)

Score: 1/1

8. Death Classification Interpretation (1 point)

Score: 1/1

Plot Assessment

1. PCA Plots (1 point)

Score: 1/1

2. Volcano Plot (1 point)

Score: 0.5/1 Feedback:

• Uses raw p-value instead of adjusted p-value (padj) for y-axis

Total Score: 9/10

[jonathanfischer97]

Grading Assessment for Daniel Mendoza

R Script Components

1. Data Loading and DESeq2 Object (1 point)

Score: 1/1

2. VST and PCA Implementation (1 point)

Score: 1/1

3. PCA Interpretation (1 point)

Score: 1/1

4. Differential Expression Analysis (1 point)

Score: 1/1

5. Sex DE Results (1 point)

Score: 1/1

6. Sex DE Interpretation (1 point)

Score: 1/1

7. Death Classification Analysis (1 point)

Score: 1/1

8. Death Classification Interpretation (1 point)

Score: 1/1

Plot Assessment

1. PCA Plots (1 point)

Score: 1/1

2. Volcano Plot (1 point)

Score: 0.5/1 Feedback:

• Using overly stringent thresholds (padj < 1e-20 instead of < 0.1, and |log2FC| > 2 instead of > 1)
• This results in fewer genes being highlighted as significant than should be

Total Score: 9.5/10