Hi. On Wed, Aug 19, 2009 at 10:53 AM, Suleiman Khan<khan.sulei...@gmail.com> wrote: > Hi, > I have run the complete "Total Copy Number Analysis" tutorial and it > works fine. > http://groups.google.com/group/aroma-affymetrix/web/total-copy-number-analysis-6-0 > > The raw CNs extracted as result of rawCNs <- as.data.frame(rawCNs), > have a chromosomal location and a copy number value. What I need is > the starting and ending location on the chromosomes for each copy > number value(i.e. starting base pair location and ending base pair > location). I have searched and tried for several hours, but wasn't > able to find.
All probes on Affymetrix chips are 25-mers (except for the most recent Cytogenetics_Array chip type where it may vary in approx 25-50mers; don't remember the details). All CN probes are single probes, thus they stretch 25 bases. For the GenomeWideSNP_6 chip type, all SNP probes are technical replicates and therefore located at the same position. Hence, the SNP loci are also 25 bases wide. I'm sure what the exact definition of the genomic location of a CN/SNP locus is in Affymetrix' NetAffx annotation data, e.g. always in the center, always at the one end, always at the SNP location for SNPs, but they are for sure reported within the 25 bases. Knowing the exact beginning and end of these loci will not make any difference in regular CN segmentation analysis. Even with perfect signals, the distance between loci are ~1.5kb, which means that the optimal segmentation precision is of that order. So, it is not possible to have the beginning and end reported of loci and I mean it is of little interest too. Hope this helps /Henrik > > Ex: > output from print(rawCNs) is: > x cn > 55765 0.7987 > 789799 -0.80980 > > What I want is > start end cn > 55765 55800 0.7987 > 789799 790011 -0.80980 > > Thanks in advance, > Suleiman > --~--~---------~--~----~------------~-------~--~----~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
