Description Usage Arguments Value Examples
description
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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). |
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. |
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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"))
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