library("aroma.affymetrix");
library("ACNE");
log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE);
dataSetName <- "Affymetrix_2006-TumorNormal";
chipType <- "Mapping250K_Nsp";
pairs <- matrix(c(
"CRL-2325D", "CRL-2324D",
"CRL-5957D", "CRL-5868D",
"CCL-256.1D", "CCL-256D",
"CRL-2319D", "CRL-2320D",
"CRL-2362D", "CRL-2321D",
"CRL-2337D", "CRL-2336D",
"CRL-2339D", "CRL-2338D",
"CRL-2341D", "CRL-2340D",
"CRL-2346D", "CRL-2314D"
), ncol=2, byrow=TRUE);
colnames(pairs) <- c("normal", "tumor");
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Setting up data set
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
cdf <- AffymetrixCdfFile$byName(chipType);
csR <- AffymetrixCelSet$byName(dataSetName, cdf=cdf);
print(csR);
# Reorder arrays according to 'pairs' matrix
csR <- extract(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 <- NmfSnpPlm(csN, mergeStrands=TRUE);
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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