library(tidyverse)
pcr_data <- read_csv("https://denvirlab.marshall.edu/BMR617-2023/data/M-F_a2d1_qPCR_quant.csv") 

pcr_data

pcr_data <- pcr_data %>% mutate(DeltaCT = a2d1_CT - GAPDH_CT)

pcr_data %>% mutate(ExpRelGAPDH = 2^-DeltaCT)

f_delta_CTs <- pcr_data %>% filter(Sex == "F") %>% pull(DeltaCT)
callibrator <- mean(f_delta_CTs)

callibrator

pcr_data <- pcr_data %>% mutate(DeltaDeltaCT = DeltaCT - callibrator)
pcr_data <- pcr_data %>% mutate(RelativeExpression = 2^-DeltaDeltaCT)

pcr_data %>% group_by(Sex) %>% 
  summarise(DeltaDeltaCT = mean(DeltaDeltaCT), RelativeExpression = mean(RelativeExpression))

t.test(DeltaCT ~ Sex, data=pcr_data)
t.test(RelativeExpression ~ Sex, data=pcr_data)

ggplot(pcr_data, aes(x=Sex, y=RelativeExpression)) + geom_boxplot(outlier.shape=NA) + geom_point(position=position_jitter(width=0.1))