Nothing
library("aroma.affymetrix")
log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
dataSetName <- "Affymetrix_2006-TumorNormal"
chipType <- "Mapping250K_Nsp"
pairs <- matrix(c(
"CRL-2325D", "CRL-2324D",
"CRL-5957D", "CRL-5868D",
"CCL-256.1D", "CCL-256D",
"CRL-2319D", "CRL-2320D",
"CRL-2362D", "CRL-2321D",
"CRL-2337D", "CRL-2336D",
"CRL-2339D", "CRL-2338D",
"CRL-2341D", "CRL-2340D",
"CRL-2346D", "CRL-2314D"
), ncol=2, byrow=TRUE)
colnames(pairs) <- c("normal", "tumor")
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Setting up data set
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
cdf <- AffymetrixCdfFile$byChipType(chipType)
csR <- AffymetrixCelSet$byName(dataSetName, cdf=cdf)
print(csR)
# Reorder arrays according to 'pairs' matrix
csR <- csR[indexOf(csR, pairs)]
acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2")
print(acc)
csC <- process(acc, verbose=log)
print(csC)
bpn <- BasePositionNormalization(csC, target="zero")
print(bpn)
csN <- process(bpn, verbose=log)
print(csN)
plm <- RmaCnPlm(csN, mergeStrands=TRUE, combineAlleles=FALSE)
print(plm)
fit(plm, verbose=log)
ces <- getChipEffectSet(plm)
print(ces)
fln <- FragmentLengthNormalization(ces, target="zero")
print(fln)
cesN <- process(fln, verbose=log)
print(cesN)
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