Hi, I´m working with the following vignette (with the 100k platform):
library(aroma.affymetrix)
#SetUp
verbose <- Arguments$getVerbose(-8)
timestampOn(verbose)
name <- "controles"
chipTypes <- c("Mapping50K_Hind240", "Mapping50K_Xba240")
cdfs <- lapply(chipTypes, FUN=function(chipType) {
AffymetrixCdfFile$byChipType(chipType)
})
print(cdfs)
gis <- lapply(cdfs, getGenomeInformation)
print(gis)
sis <- lapply(cdfs, getSnpInformation)
print(sis)
cesNList <- list()
chipType <- chipTypes[1]
cs <- AffymetrixCelSet$byName(name, chipType=chipType)
cs <- extract(cs, !isDuplicated(cs))
print(cs)
qn <- QuantileNormalization(cs)
print(qn)
csN <- process(qn, verbose=-20)
plm <- RmaCnPlm(csN, combineAlleles=TRUE, mergeStrands=TRUE)
print(plm)
fit(plm, verbose=-20)
ces <- getChipEffectSet(plm)
fln <- FragmentLengthNormalization(ces)
print(fln)
cesNList[[chipType]] <- process(fln, verbose=verbose)
chipType <- chipTypes[2]
cs <- AffymetrixCelSet$byName(name, chipType=chipType)
cs <- extract(cs, !isDuplicated(cs))
print(cs)
qn <- QuantileNormalization(cs)
print(qn)
csN <- process(qn, verbose=-20)
plm <- RmaCnPlm(csN, combineAlleles=TRUE, mergeStrands=TRUE)
print(plm)
fit(plm, verbose=-20)
ces <- getChipEffectSet(plm)
fln <- FragmentLengthNormalization(ces)
print(fln)
cesNList[[chipType]] <- process(fln, verbose=verbose)
glad <- GladModel(cesNList)
print(glad)
ce <- ChromosomeExplorer(glad)
setArrays(ce, c("R007", "R014", "R015", "R035", "R039", "R052",
"R062", "R064", "R072", "R075", "R081", "R102", "R106", "R108",
"R111", "R115", "R121", "R124", "R183", "R189", "R208", "R221",
"R230", "R240", "R247", "R208"))
setAlias(ce, "Oscar_controls_2009")
print(ce)
process(ce, chromosomes=c
(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23),verbose=verbose)
My experiment was designed for 27 tumors. It runs without errors but I
´m obtaining chromosomes complete gain or lost
I wonder if I´m doing it right or I´m missing something or the number
of experiments is not enough to find something significant. I´m
comparing my results against a CNAT results and the number of segments
are too much diferent.
Thx in advance
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