Lab 11: Differential Gene Expression Flashcards
Use R to analyze Gene Sets
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
Describe Differential Expression Analysis
Differential Expression analysis is searching for difference in gene expression. The program used is DESeq2
Create and analyze histograms from HTSeq files
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.
Calculate Differential Gene Expression in real scientific data