Henrik
seems like it does not work. I went on to R2.9.0 with latest version
of aroma but I get the following:
I tried also the getAverageFile() function but with the same result. I
guess the two functions do the same thing or a very similar one?
Marco
cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6",
tags="Full")
print(cdf)
gi <- getGenomeInformation(cdf)
print(gi)
si <- getSnpInformation(cdf)
print(si)
cs <- AffymetrixCelSet$byName("POOLS", cdf=cdf)
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))
#ceR1 <- calculateBaseline(ces1,chromosomes=1:24,
ploidy=2,defaultPloidy=2, verbose=verbose);
#ceR2 <- calculateBaseline(ces2,chromosomes=1:24,
ploidy=2,defaultPloidy=2, verbose=verbose);
ceR1 <- getAverageFile(ces1, verbose=verbose)
ceR2 <- getAverageFile(ces2, verbose=verbose)
cbs <- CbsModel(ceR1,ceR2)
> cbs <- CbsModel(ceR1,ceR2)
Error in list(`CbsModel(ceR1, ceR2)` = <environment>, `extend
(CopyNumberSegmentationModel(cesTuple = cesTuple, ...), "CbsModel")` =
<environment>, :
[2009-06-09 20:49:14] Exception: Argument 'csList' contains a non-
ChipEffectSet: CnChipEffectFile
at throw(Exception(...))
at throw.default("Argument 'csList' contains a non-", .setClass, ":
", class(c
at throw("Argument 'csList' contains a non-", .setClass, ": ", class
(cs)[1])
at AromaMicroarrayDataSetTuple(..., .setClass = .setClass)
at extend(AromaMicroarrayDataSetTuple(..., .setClass = .setClass),
"Affymetrix
at AffymetrixCelSetTuple(csList = csList, ..., .setClass
= .setClass)
at extend(AffymetrixCelSetTuple(csList = csList, ..., .setClass
= .setClass),
at ChipEffectSetTuple(cesTuple)
at CopyNumberChromosomalModel(...)
at extend(CopyNumberChromosomalModel(...),
"CopyNumberSegmentationModel")
at CopyNumberSegmentationModel(cesTuple = cesTuple, ...)
at extend(CopyNumberSegmentationModel(cesTuple = cesTuple, ...),
"CbsModel")
at CbsModel(ceR1, ceR2)
> sessionInfo()
R version 2.9.0 (2009-04-17)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices datasets utils methods
base
other attached packages:
[1] DNAcopy_1.18.0 aroma.affymetrix_1.1.0
aroma.apd_0.1.3
[4] R.huge_0.1.7 affxparser_1.16.0
aroma.core_1.1.0
[7] aroma.light_1.13.2 matrixStats_0.1.5
R.rsp_0.3.4
[10] R.filesets_0.5.1 digest_0.3.1
R.cache_0.1.7
[13] R.utils_1.1.6 R.oo_1.4.6
R.methodsS3_1.0.3
[16] EBImage_3.0.1 abind_1.1-0
On 9 Juni, 03:05, Henrik Bengtsson <h...@stat.berkeley.edu> wrote:
> Hi.
>
>
>
> On Mon, Jun 8, 2009 at 1:53 PM, marco<mazu.c...@gmail.com> wrote:
>
> > 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)
>
> Yes, your script seems to do the correct thing; preprocess all arrays
> as if they are from independent samples and then average
> (calculateBaseline) within each group.
>
> You probably want to update the above to chromosomes=1:24, or simply
> drop the argument because it defaults to use all chromosomes.
>
> FYI, use byChipType() and byName() - the fromNnn() names are deprecated.
>
> Also, you are using an old version of CRMA for processing
> GenomeWideSNP_6 arrays; there is a much better CRMA v2 available. See
> online Vignette 'Estimation of total copy numbers using the CRMA v2
> method':
>
> http://groups.google.com/group/aroma-affymetrix/web/estimation-of-tot...
>
> /Henrik
>
>
>
> > Best Regards
>
> > Marco
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