Hi all,


I have already obtained a data set from Illumina Beadchip-HT12 experience
and I would like to analyse them in R with Beadarray package. I have files
with the following extensions (.txt, .csv, .idat, .xml, .locs, .tiff) with a
text file called Metrics. I guess that only two files are required (.txt and
.tiff), right ?
Now, I try to use the following script, wrote by Mark Dunning (thanks for
him!) but I don't get what I should to get! Surely because the formats are
not the same between the new HumanV3 beadchip I use and the previous one
(HumanV2 for which the script was written) !
Here is the program and I will be grateful if somebody could tell me where
in the script and what I have to change to adapt it my HumanHT12 beadchip?

targets = read.table("targets.txt", sep = "\t", header = TRUE,
as.is = TRUE)
dir()
targets = read.table("targets.txt", sep = "\t", header = TRUE,
as.is = TRUE)
Metrics = read.table("targets.txt", sep = "\t", header = TRUE,
as.is=TRUE)
Metrics = read.table("Metrics.txt", sep = "\t", header = TRUE,
as.is=TRUE)
Metrics
BLData <- readIllumina(textType = ".csv", backgroundMethod = "none",
targets = targets, arrayNames = targets$ArrayName, metrics = TRUE)
 BLData <- readIllumina(textType = ".csv", backgroundMethod = "none",
Matrics = Matrics, arrayNames = Metrics$ArrayName, metrics = TRUE)
is(BLData)
class(BLData)
slotNames(BLData)
an = arrayNames(BLData)
an
names(BLData@beadData[[an[1]]])
BLData[[an[1]]]$G[1:10]
BLData[[an[2]]]$Gb[1:10]
pData(BLData)
getArrayData(BLData, array = 1, what = "G", log = FALSE)[1:10]
getArrayData(BLData, array = 2, what = "Gb", log = FALSE)[1:10]
par(mfrow = c(1, 3))
boxplotBeads(BLData, las = 2, outline = FALSE, ylim = c(4, 12),
main = "Foreground")
boxplotBeads(BLData, las = 2, whatToPlot = "Gb", outline = FALSE,
ylim = c(4, 12), main = "Background")
BLData.bc = backgroundCorrect(BLData, method = "subtract")
boxplotBeads(BLData.bc, las = 2, outline = FALSE, ylim = c(4,
12), main = "Background Corrected")
ids = unique(BLData[[an[1]]]$ProbeID)[1:10]
ids
ProbeCols = rainbow(10)
plotBeadIntensities(BLData, arrays = c(1, 3), ProbeIDs = ids,
ProbeCols = ProbeCols, log = TRUE, ylim = c(8, 15))
ProbeCols = rainbow(10)
> plotBeadIntensities(BLData, arrays = c(1, 3), ProbeIDs = ids,
+ ProbeCols = ProbeCols, log = TRUE, ylim = c(8, 15))ProbeCols = rainbow(10)
plotBeadIntensities(BLData, arrays = c(1, 3), ProbeIDs = ids,
ProbeCols = ProbeCols, log = TRUE, ylim = c(8, 15))
o = findAllOutliers(BLData, array = 1)
o[1:10]
length(o)/numBeads(BLData)[1]
par(mfrow = c(2, 1))
par(mar = c(1, 1, 3, 1))
for (i in 1:2) {
o = findAllOutliers(BLData, array = i)
plotBeadLocations(BLData, BeadIDs = o[1:1000], array = i,
SAM = FALSE, cex = 0.5, col = "red", pch = 16)
}
par(mfrow = c(2, 1))
for (i in 1:2) {
imageplot(BLData, array = i, nrow = 20, ncol = 200, zlim = range(9,
10), low = "yellow", high = "red", what = "G")
}


Thank you very much

Leon

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