highSCREEN (version 0.4)

normplate: Normalize plate

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

# NOT RUN {
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"))
# }