[BioC] Problem with Beadarray package for beadchipHT-12

[Perry Moerland]

Hi Leon,
Could you tell us where your code stops working, include the error 
message, and also include a sessionInfo(), otherwise it will be hard to 
give you any input.
best
Perry

Leo Nitsche wrote:
> 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 at 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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> 
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-- 
Perry Moerland, PhD
Room J1B-206, Bioinformatics Laboratory
Department of Clinical Epidemiology, Biostatistics and Bioinformatics
Academic Medical Centre, University of Amsterdam
Postbus 22660, 1100 DD Amsterdam, The Netherlands
tel: +31 20 5664660
p.d.moerland at amc.uva.nl, http://www.amc.uva.nl/