The data set consists of observations of the expression levels of 8,993 genes at 6 time points in 6 mice.
Dr. Julie Wilder (Lovelace Respiratory Research Institute) studies the response of the lung to the introduction of pathogens. In particular, she has examined the genetic characteristics of immune response to infection with the pathogen Cryptococcus neoformans in mice. A preliminary study indicated that differences in the ability of two strains of mice, C57BL/6 and C.B-17, to clear the pathogen from the lung were likely due to genetic causes.
One component of Dr. Wilder’s overall study was the use of microarray data to determine which genes show differential expression between the two strains of mice as a function of time following infection with C. neoformans. For each strain of mouse, she used three microarrays at each of six time points: 0, 6 hours, 24 hours, 72 hours, 7 days, and 14 days post-infection. This is a total of 2 \(\times\) 3 \(\times\) 6 = 36 arrays.
In this assignment, you will try to determine which genes show differential expression between the two groups of mice and at which time points.
| Variable | Description |
|---|---|
Name |
List of gene names |
b6ijs |
Gene expression value for C57BL/6 mouse \(j\) at time point \(i\) |
cbijs |
Gene expression value for C.B-17 mouse \(j\) at time point \(i\) |
mouse_data = read.table("data/MouseGeneExpression2B.txt", header = TRUE)
head(mouse_data)Within each time point, two-sample t-tests can be used to compare the expression levels of each gene in the C57BL/6 vs. C.B-17 mice. However, this will amount to carrying out \(8,993 \times 6\) separate hypothesis tests. This project explores the feasibility of searching for genes that show differential expression in the two groups in this way.