Description Usage Arguments Details Value References Examples
description
1 2 | qcplate(dat, s0="S0", s1="S1", poscont="Control P",
negcont="Control N", qc1.val=0.225, qc2.val=2, addcont, welltype="welltype")
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dat |
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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. |
details
value
references
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 | 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")
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