Hi People,
I have the following sequence of commands:
chipType <- "GenomeWideSNP_5";
cdfTags <- "Full,r2";
cdf <- AffymetrixCdfFile$byChipType(chipType, tags=cdfTags)
print(cdf)
gi <- getGenomeInformation(cdf)
print(gi)
si <- getSnpInformation(cdf)
print(si)
acs <- AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE))
print(acs)
csR <- AffymetrixCelSet$byName("sleData", cdf=cdf)
print(csR)
acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2")
print(acc)
csC <- process(acc, verbose=verbose)
print(csC)
bpn <- BasePositionNormalization(csC, target="zero")
print(bpn)
csN <- process(bpn, verbose=verbose)
print(csN)
plm <- AvgCnPlm(csN, mergeStrands=TRUE, combineAlleles=TRUE, shift=+300)
print(plm)
fit(plm, verbose=verbose)
ces <- getChipEffectSet(plm)
print(ces)
fln <- FragmentLengthNormalization(ces, target="zero")
print(fln)
cesN <- process(fln, verbose=verbose)
print(cesN)
ceR <- getAverageFile(cesN, verbose=verbose)
print(ceR)
cbs <- CbsModel(cesN)
print(cbs)
chrs<-seq(1,22)
fit(cbs,chromosomes=chrs,verbose=verbose)
ce <- ChromosomeExplorer(cbs)
print(ce)
process(ce, chromosomes=chrs, verbose=verbose)
The last command creates a number of graphic files, each of which
displays the estimate of standard errors (\hat\sigma_{\delta}). Is
there any way to get these estimates as a sequence of numbers
corresponding to each “mean” in the “regions.xls”?
Thanks
Max
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