Hi David, First, a remark: it seems you're using CRMA v1; I recommend that you use CRMA v2 instead, see this vignette:
http://groups.google.com/group/aroma-affymetrix/web/estimation-of-total-copy-numbers-using-the-crma-v2-method At the end of this vignette there is a paragraph explaining how to plot total copy numbers along a chromosome. You can do the same with your current 'cesN', i.e. : ## define units of interest units <- getUnitsOnChromosome(gi, chromosome=2, region=c(81,86)*1e6) pos <- getPositions(gi, units=units) ## get the estimates for the first array ce <- getFile(cesN, 1) theta <- extractTheta(ce, units=units) 'pos' contains the position of the SNP, and 'theta' the normalized (total) intensities. Alternatively you can also do df <- extractChromosomalDataFrame(ce, units=units) which with the data of the above vignette will look like: > str(df) > 'data.frame': 2901 obs. of 6 variables: $ unit : int 1035784 1035785 776062 742910 1035786 1035783 1035788 419702 1035789 1035790 ... $ group : int 1 1 1 1 1 1 1 1 1 1 ... $ cell : int 1976248 1976249 1551502 1485198 1976250 1976247 1976252 838782 1976253 1976254 ... $ chromosome : int 2 2 2 2 2 2 2 2 2 2 ... $ physicalPosition: int 81001208 81001975 81005617 81006134 81009408 81009733 81016544 81016718 81017018 81023108 ... $ NA06985 : num 1817 778 2586 3323 1080 ... You can also do this for all arrays at once: df <- extractChromosomalDataFrame(cesN, units=units) Cheers, Pierre. On Thu, May 14, 2009 at 10:59 AM, David <daescarc...@gmail.com> wrote: > > Hi Henrik! > > I´m working with the following vignette ( for the Affymetrix 5.0): > > library(aroma.affymetrix) > verbose <- Arguments$getVerbose(-8, timestamp=TRUE) > cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_5", tags="Full,r2") > print(cdf) > gi <- getGenomeInformation(cdf) > print(gi) > cs <- AffymetrixCelSet$byName("tumoresAna", 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) > > Everything runs! > > But from this point forward I would like to analyze data, SNP by SNP, > so: > > I wonder how could I analyze the intensity value of each SNP? > How could I read both values, the normalized intensity and the locus > for each SNP? > I would like to see all markers as a sequence. > > Thx in advance! > > David > > > --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
