normplate: Normalize plate

In highSCREEN: High-Throughput Screening for Plate Based Essays

Description

description

Usage

normplate(mainplate, dat0, dat1, cmap, plate, replicate, norm="bscore",
 poscont=NULL, negcont=NULL)

Arguments

mainplate	Main Plate designation.
dat0	Data frame containing the 96-well t0-specific plate/quadrant to be normalized.
dat1	Data frame containing the 96-well t1-specific plate/quadrant to be normalized.
cmap	96-well plate control map.
plate	Plate/quadrant designation. Ranges from 1 to 4.
replicate	Replicate designation.
norm	Normalization method to be applied. Currenlty implemented methods include C-score (cscore), B-score (bscore), Z-score (eqnzscore) and no normalization (raw).
poscont	Specifies positive control designation (used in C-score normalization).
negcont	Specifies negative control designation (used in C-score normalization).

Value

Data frame containing the following columns:

MainPlate	Specifies the main plate to wich the compound/control belongs.
Time	Specifies t0 (0) or t1 (1) specific data.
Plate	Specifies the quadrant/plate to wich the compound/control belongs.
Replicate	Specifies replicate.
Norm	Specifies the normalization method that was applied for the specific compound.
well	Specifies the location (row and column) of the compound/control in the quadrant.
row	Specifies the row location in the quadrant.
col	Specifies the column location in the quadrant.
score	Shows the score value.
welltype	Specifies if the well is compound or control.

Examples

set.seed(1234)
nc = 24
nr = 16

# create control map
cmap = data.frame(X1=c(rep("Control P", floor(nr/3)), 
rep(c("Control low", "Control med", "Control high"), 
(floor(nr/3)+nr-3*floor(nr/3))/3), rep("Control N", 
floor(nr/3))), X2=c(rep("Control N", floor(nr/3)), 
rep(c("Control low", "Control med", "Control high"), 
(floor(nr/3)+nr-3*floor(nr/3))/3), rep("Control P", floor(nr/3))))
cmap = cmap[seq(1,nr,2),]
cmap

# create 1st replicate of data matrix with compounds and controls
r1 = matrix(abs(rnorm(nr*nc)), nr, nc)

# create 2nd replicate of data matrix with compounds and controls
r2 = matrix(abs(rnorm(nr*nc)), nr, nc)

# create 3rd replicate of data matrix with compounds and controls
r3 = matrix(abs(rnorm(nr*nc)), nr, nc)

# combine all replicate for the t0-specific data
replicates_t0 = list(r1, r2, r3)
names(replicates_t0) = c("R1", "R2", "R3")

# create 1st replicate of data matrix with compounds and controls
r1 = matrix(abs(rnorm(nr*nc)), nr, nc)

# create 2nd replicate of data matrix with compounds and controls
r2 = matrix(abs(rnorm(nr*nc)), nr, nc)

# create 3rd replicate of data matrix with compounds and controls
r3 = matrix(abs(rnorm(nr*nc)), nr, nc)

# combine all replicate for the t1-specific data
replicates_t1 = list(r1, r2, r3)
names(replicates_t1) = c("R1", "R2", "R3")

# extract plate 1, replicate 1
dat = extractplate(replicates_t0, replicates_t1, plate=1, replicate=1)

# normalize using c-score
head(normplate("Main Plate 1", dat[["dat0"]], dat[["dat1"]], cmap, 
plate=1, replicate=1, norm="cscore",
 poscont="Control P", negcont="Control N"))

# normalize using b-score (medpolish)
head(normplate("Main Plate 1", dat[["dat0"]], dat[["dat1"]], cmap, 
plate=1, replicate=1, norm="bscore"))

# normalize using z-score
head(normplate("Main Plate 1", dat[["dat0"]], dat[["dat1"]], cmap, 
plate=1, replicate=1, norm="zscore"))

highSCREEN documentation built on Feb. 12, 2021, 5:09 p.m.