Make sure to not delete or alter the questions Follow the instructions on the code and answer the qu

INSTRUCTIONS TO CANDIDATES

ANSWER ALL QUESTIONS

Make sure to not delete or alter the questions Follow the instructions on the code and answer the questions. Use the link of lab 4, lab 6, Lab 7, Lab 8, Lab 9, and exam 2 as a reference for what was wrong before. Give me the Rcode when done

 

Exam III Outline – Gene Expression Analysis

1. Different ways of coding explanatory variables in linear models

2. Relationship between two-sample t-test and a linear model with coded

variables using treatment contrasts (x = 0 and x = 1).

3. RNA-seq biology (read counts)

4. Processing of RNA-seq data: FPKM/RPKM, TMM, and TMM

5. Retrieving data using the UCSCXenaTools R package

6. Understanding the format of RNA-seq data and accessing clinical

(phenotype) variables

7. Constructing side-by-side boxplots comparing the gene expression across

groups

8. Identifying differentially expressed probes/genes using the limma package

and understanding the false discovery rate (FDR)

9. Generating heatmaps

10. Converting a probe name to the corresponding gene symbol and vice versa

using the probe map data provided by UCSC Xena

11. Classification using k-nearest neighbors (knn), including leave-one-out crossvalidation, optimization, and making predictions in a test dataset.

12. Perform a gene set enrichment analysis using DAVID, based on a list of genes

 

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