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 -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/