title | author | date |
---|---|---|
Spect.Rmd |
Shuce Zhang |
2018/5/4 |
This script is to analyze spectrum data from plate readers. Should you have any questions please contact Shuce: shuce@ualberta.ca
- Right-click
test/raw.txt
to open in MS Excel, paste your data in, and save. Your data will be saved in tab-delimited formats. - First time you run the script with
do_norm
set to FALSE. You can find the peak heights in the summary, which you may want to use as your normalization factors. Editnorm_vec
accordingly, and then turn thedo_norm
to TRUE or 1. - General users should focus on the parameters part. Do not mess up with the functions. If you would like to implement new tasks, write new functions for them.
You can customize this part to adapt to your experiments.
setwd("G:/GitHub/Spectrum/test") # working directory
#raw <- read.table("raw.txt", header = TRUE) # input file
init.df <- read.table("raw.txt", header = TRUE)
blank <- init.df$H7 # identify the background well
wav <- init.df[,1]
raw <- init.df[,2:ncol(init.df)] - blank
raw <- data.frame(wav, raw)
raw$A7 <- NULL # Remove the background wells
raw$H7 <- NULL # Remove the background wells
colNum <- ncol(raw)
reorg <- 0 # 0 if replication are in the same row, 1 if same column
reorg.rep <- 3 # number of samples
norm_wav_range <- c(350,390) # range of peaks you want to label
do_norm <- FALSE # 1 if you want to output normalized data
# normalization factor for each sample.
# Measurements of each sample will be divided by these values, respectively
norm_vec <- c(0.083, 0.200, 0.043, 0.152, 0.169, 0.192,
0.210, 0.213, 0.216, 0.206, 0.193, 0.216,
0.144, 0.207, 0.227, 0.196, 0.189, 0.204,
0.253, 0.240, 0.217, 0.117, 0.194, 0.193,
0.182, 0.191, 0.196, 0.210, 0.185, 0.196,
0.168, 0.195, 0.086, 0.204, 0.177, 0.225,
0.216, 0.163, 0.521, 0.210, 0.278, 0.230,
0.274, 0.246, 0.234, 0.232, 0.252, 0.310)
#0.199, 0.183, 0.183, 1, 0.281, 0.291, 1)
#norm_update <- t(raw[11,2:colNum])
#rownames(norm_update) <- c()
#norm_vec <- norm_update # Comment if you want to use the old coefficents