Dear Henrik,
In analyzing some copy number data from chromosome 14, I noticed that
there are 57,103 loci for the Affy 6.0 array, however, only 56,980 of
these loci have unique positions. Here is the proof from R
> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full")
> gi <- getGenomeInformation(cdf)
> units <- getUnitsOnChromosome(gi, chromosome=14)
> pos <- getPositions(gi, units=units)
> length(pos)
[1] 57103
> length(unique(pos))
[1] 56980
> sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] aroma.affymetrix_1.7.0 aroma.apd_0.1.7
affxparser_1.20.0
[4] R.huge_0.2.0 aroma.core_1.7.0
aroma.light_1.16.1
[7] matrixStats_0.2.1 R.rsp_0.3.6
R.cache_0.3.0
[10] R.filesets_0.8.3 digest_0.4.2
R.utils_1.5.0
[13] R.oo_1.7.3 R.methodsS3_1.2.0
Shouldn't all the loci have different positions in bps? Note, the
duplicate positions seem to correspond to different raw CN
estiamtes.This is a problem for me because my hidden Markov model
doesnt work when I have multiple observations with the same positions.
Thanks for you assistance.
Matt
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