Dear Henrik,
I have 2 samples hzbridiyed on SNP6 in respctively 5 and 6
replicates. I would like to pool them ann estimate the relative CNVs.
Is this fragment of code doing that? Or you have any other
suggestions?
cdf <- AffymetrixCdfFile$fromChipType("GenomeWideSNP_6",
tags="Full")
print(cdf)
gi <- getGenomeInformation(cdf)
print(gi)
si <- getSnpInformation(cdf)
print(si)
cs <- AffymetrixCelSet$fromName("POOLS", cdf=cdf,verbose=-20)
print(cs)
acc <- AllelicCrosstalkCalibration(cs)
print(acc)
csC <- process(acc, verbose=verbose)
print(csC)
plm <- AvgCnPlm(csC, mergeStrands=TRUE, combineAlleles=TRUE,
shift=+300)
print(plm)
fit(plm, verbose=verbose)
ces <- getChipEffectSet(plm)
print(ces)
fln <- FragmentLengthNormalization(ces)
print(fln)
cesN <- process(fln, verbose=verbose)
print(cesN)
ces1 <- extract(cesN,c(1:5))
ces2 <- extract(cesN,c(6:11))
ceRef1 <- calculateBaseline(ces1,chromosomes=1:23,
ploidy=2,defaultPloidy=2, verbose=verbose);
ceRef2 <- calculateBaseline(ces2,chromosomes=1:23,
ploidy=2,defaultPloidy=2, verbose=verbose);
cbs <- CbsModel(ces1,ces2)
ce <- ChromosomeExplorer(cbs)
print(ce)
process(ce, chromosomes=c(1:23), verbose=verbose)
Best Regards
Marco
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