highSCREEN (version 0.4)

qcplate: Quality control

Description

description

Usage

qcplate(dat, s0="S0", s1="S1", poscont="Control P",
 negcont="Control N", qc1.val=0.225, qc2.val=2, addcont, welltype="welltype")

Arguments

dat

s0

Specifies the name of the columns containing t0-specific scores.

s1

Specifies the name of the columns containing t1-specific 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

# NOT RUN {
set.seed(1234)
nc = 24
nr = 16

# create 1st replicate of data matrix with compounds and controls
r1 = 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 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 replicates for the t0-specific data
replicates_t0 = list(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 replicates for the t1-specific data
replicates_t1 = list(r1, r2, r3)
names(replicates_t1) = c("R1", "R2", "R3")

# extract plate 1, replicate 1
dat11 = extractplate(replicates_t0, replicates_t1, plate=1, replicate=1)

# extract plate 1, replicate 2
dat12 = extractplate(replicates_t0, replicates_t1, plate=1, replicate=2)

# extract plate 1, replicate 3
dat13 = extractplate(replicates_t0, replicates_t1, plate=1, replicate=3)

# no normalizion (norm="raw")
res11 = normplate("Main Plate 1", dat11[["dat0"]], dat11[["dat1"]], cmap,
 plate=1, replicate=1, norm="raw")
res12 = normplate("Main Plate 1", dat12[["dat0"]], dat12[["dat1"]], cmap,
 plate=1, replicate=2, norm="raw")
res13 = normplate("Main Pltae 1", dat13[["dat0"]], dat13[["dat1"]], cmap,
 plate=1, replicate=3, norm="raw")

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

# reformat result
res1 = formatRESULT(res1, replicate="Replicate", 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")
# }