highSCREEN (version 0.1)

normplate: title

Description

description

Usage

normplate(mainplate, datbefore, datafter, cmap, plate, triplicate, norm="bscore", poscont=NULL, negcont=NULL)

Arguments

mainplate

Main Plate designation.

datbefore

Data frame containing the 96-well "Before" plate/quadrant to be normalized.

datafter

Data frame containing the 96-well "After" plate/quadrant to be normalized.

cmap

96-well plate control map.

plate

Plate/quadrant designation. Ranges from 1 to 4.

triplicate

Triplicate designation. Ranges from 1 to 3.

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 "Before" or "After".

Plate

Specifies the quadrant/plate to wich the compound/control belongs.

Triplicate

Specifies triplicate.

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
replicate1 = matrix(abs(rnorm(nr*nc)), nr, nc)

# create 2nd replicate of data matrix with compounds and controls
replicate2 = matrix(abs(rnorm(nr*nc)), nr, nc)

# create 3rd replicate of data matrix with compounds and controls
replicate3 = matrix(abs(rnorm(nr*nc)), nr, nc)

# combine all replicate for the before data
replicates_before = list(replicate1, replicate2, replicate3)
names(replicates_before) = c("Replicate1", "Replicate2", "Replicate3")

# create 1st replicate of data matrix with compounds and controls
replicate1 = matrix(abs(rnorm(nr*nc)), nr, nc)

# create 2nd replicate of data matrix with compounds and controls
replicate2 = matrix(abs(rnorm(nr*nc)), nr, nc)

# create 3rd replicate of data matrix with compounds and controls
replicate3 = matrix(abs(rnorm(nr*nc)), nr, nc)

# combine all replicate for the after data
replicates_after = list(replicate1, replicate2, replicate3)
names(replicates_after) = c("Replicate1", "Replicate2", "Replicate3")

# extract plate 1, replicate 1
dat = extractplate(replicates_before, replicates_after, plate=1, replicate=1)

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

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

# normalize using z-score
head(normplate("Main Plate 1", dat[["datbefore"]], dat[["datafter"]], cmap, 
plate=1, triplicate=1, norm="zscore"))