highSCREEN (version 0.1)

qcplate: title

Description

description

Usage

qcplate(dat, score.before="scorebefore", score.after="scoreafter", poscont="Control P", negcont="Control N", qc1.val=0.225, qc2.val=2, addcont, welltype="welltype")

Arguments

dat

score.before

Specifies the name of the columns containing "Before" scores.

score.after

Specifies the name of the columns containing "After" scores.

poscont

Specifies positive control designation (used in C-score normalization).

negcont

Specifies negative control designation (used in C-score normalization).

qc1.val

Pre-defined threshold value for QC1.

qc2.val

Pre-defined threshold value for QC2.

addcont

A vector character names specifying the additional controls for QC3. The vignette provides more details on the particular order of specifying the additional controls.

welltype

Specifies the name for the column defining the well type.

Value

value

Details

details

References

references

Examples

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

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

# 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),]

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

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

# combine all triplicates for the before data
replicates_before = list(replicate1, replicate2, replicate3)

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

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

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

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

# extract plate 1, replicate 1
dat11 = extractplate(replicates_before, replicates_after, plate=1, replicate=1)

# extract plate 1, triplicate 2
dat12 = extractplate(replicates_before, replicates_after, plate=1, replicate=2)

# extract plate 1, triplicate 3
dat13 = extractplate(replicates_before, replicates_after, plate=1, replicate=3)

# no normalizion (norm="raw")
res11 = normplate("Main Plate 1", dat11[["datbefore"]], dat11[["datafter"]], cmap,
 plate=1, triplicate=1, norm="raw")
res12 = normplate("Main Plate 1", dat12[["datbefore"]], dat12[["datafter"]], cmap,
 plate=1, triplicate=2, norm="raw")
res13 = normplate("Main Pltae 1", dat13[["datbefore"]], dat13[["datafter"]], cmap,
 plate=1, triplicate=3, norm="raw")

# combine 3 replicates
res1 = rbind(res11, res12, res13)

# reformat result
res1 = formatRESULT(res1, triplicate="Triplicate", score="score", t="Time")

# perform QC
qcplate(res1, poscont="Control P", negcont="Control N", qc1.val=0.225, qc2.val=2, 
addcont=c("Control low", "Control med", "Control high"), welltype="welltype")