Lab 11: Differential Gene Expression

Question 1

Use R to analyze Gene Sets

Answer 1

Most of the time you will be using R functions to analyze your data. R functions generally take some input (usually your data) and produce some output (such as a plot).

To run a function in R, you type the name of the function followed by parentheses, and you put the input(s) to the function inside the parentheses, separated by commas:

functionName( INPUT1, INPUT2 )

Inputs tell the function how to run. For example, the summary() command needs one input: what data it should summarize. If we want a summary of our RNA-seq readCounts, we would type

Question 2

Describe Differential Expression Analysis

Answer 2

Differential Expression analysis is searching for difference in gene expression. The program used is DESeq2

Question 3

Create and analyze histograms from HTSeq files

Answer 3

HTseq aligns the sequences to the reference genome and counts how many sequences align to each gene.
More sequences align to a gene, the higher the expression level of the gene.

Question 4

Calculate Differential Gene Expression in real scientific data