Dear All,

I'm using XPS to analyse Human Exon Arrays.
I tried DABG and MAS5 to compute the detection calls and I'm getting very
different results (It seems to me that things gets scrambled at some point).

here is the code I used:

root.path <- "/home/thomas/QC.reporting/batch27/ROOT_files"
root.filename <- "batch2.root"
data.path <- "/home/thomas/QC.reporting/batch27/ROOT_files"
data.filename="data_batch27.root"
output.path <- "/home/thomas/QC.reporting/batch27/"

root.data <- load.root.data(root.path, root.filename, data.path,
data.filename)
data.rma <- rma(root.data, filedir = root.path, filename = paste("tmpdt",
"RMA", root.filename, sep="_"), tmpdir = paste(getwd(), "tmp", sep="/"),
background="antigenomic", normalize = TRUE, option = "exon", exonlevel =
"all", verbose=TRUE)
call.dabg <- dabg.call(root.data, filedir = root.path, filename =
paste("tmpdt", "RMA", root.filename, sep="_"), option = "exon", exonlevel =
"all", verbose = TRUE)
call.mas5 <- mas5.call(root.data, filedir = root.path, filename =
paste("tmpdt", "MAS5", root.filename, sep="_"), option = "exon", exonlevel =
"all", verbose = TRUE)

The parameters for each detection call:
> call.dabg@params
$alpha1
[1] 0.04

$alpha2
[1] 0.06

> call.mas5@params
$tau
[1] 0.015

$alpha1
[1] 0.04

$alpha2
[1] 0.06

$ignore
[1] TRUE

The results I obtain (in matter of Present/Marginal/Absent):
PivotTable.txt using DABG:
Parameter W764.dab W766.dab
PercentAbsent 88.6888 90.155
PercentMarginal 2.8019 2.4824
PercentPresent 8.50933 7.36258

PivotTable.txt: using MAS5
Parameter W764.dc5 W766.dc5
PercentAbsent 9.48876 9.89098
PercentMarginal 1.96661 1.96727
PercentPresent 88.5446 88.1418

The results obtained contradicts each other. Is there any reason for that?
What am I doing wrong here?

Thanks in advance for your answers.

Thomas

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