Exploratory plots of the linear mixed-effects model

Load the libraries

library(lattice)
library(VennDiagram)

Load the data

setwd('~/UBC Stats/STAT540/Group Project/')

# Load the M-values
load('Data/ALL_tall.Rdata')

# Load the results of the linear models
lm.t <- read.table('Data/lm.tab', stringsAsFactors=FALSE)
lme.t_reml <- read.table('Data/lme.tab', stringsAsFactors=FALSE)
lme.t_ml <- read.table('Data/lme_ml.tab', stringsAsFactors=FALSE)

# Load the sets gene hits
lm.geneset <- readLines('Data/lm-geneset.txt')
lme.geneset <- readLines('Data/lme-geneset.txt')

Plot the M-values of a CpG island

stripplot(M ~ Group | probe, tall,
    jitter = TRUE, auto.key = TRUE, type = c('p', 'a'),
    subset = cgi == lme.t_ml[1, 'cgi'],
    main='Strip plot of the probes of a single CpG island',
    ylab='M-value')

Plot the denisty of the q-values of the linear model

densityplot(lm.t$q,
    main='Density of q-values of the linear model',
    xlab='q-value')

Plot the denisty of the t-statistic of the linear mixed-effects model

densityplot(lme.t_reml$t,
    main='Density of the t-statistic of the linear mixed-effects model',
    xlab='t-statistic')

Venn diagram of the overlap of the hits of the fixed and mixed models

plot.new()
grid.draw(venn.diagram(list(
    LinearModel = lm.geneset,
    LinearMixedEffectsModel = lme.geneset),
    filename=NULL, fill=c('red', 'blue')))