Hi again, Henrik pointed to me that plotAllelePairs.AllelicCrosstalkCalibration has an argument 'pairs' which can be used to specify the indexes of the pairs that one wants to plot. In my case
plotAllelePairs(acc, array=array, pairs=1:6, what="input", xlim=xlim/3) does the job. Cheers, Pierre On Wed, Jan 14, 2009 at 11:56 AM, Pierre Neuvial <pie...@stat.berkeley.edu> wrote: > Hi, > > I have followed the steps of the CRMAv2 vignette: > > http://groups.google.com/group/aroma-affymetrix/web/estimation-of-total-copy-numbers-using-the-crma-v2-method > > using aroma.affymetrix version 1.0.0 and I got the following warning: > >> plotAllelePairs(acc, array=array, what="input", xlim=xlim/3) > Warning message: > In matrix(seq(length = nbrOfPairs), nrow = floor(sqrt(nbrOfPairs))) : > data length [7] is not a sub-multiple or multiple of the number of rows [2] > > This is because there are now *7* allele probe pair groups, not 6: > >> names(getSetsOfProbes(acc)$snp) > [1] "A/C" "A/G" "A/T" "C/G" "C/T" "G/T" "missing" > > As a result the plot layout is wrong: > >> nbrOfPairs <- length(getSetsOfProbes(acc)$snp) >> matrix(seq(length = nbrOfPairs), nrow = floor(sqrt(nbrOfPairs))) > [,1] [,2] [,3] [,4] > [1,] 1 3 5 7 > [2,] 2 4 6 1 > Warning message: > In matrix(seq(length = nbrOfPairs), nrow = floor(sqrt(nbrOfPairs))) : > data length [7] is not a sub-multiple or multiple of the number of rows [2] > > Maybe the easiest fix is to plot only the non "missing" allele pairs. > > Note that if one wants to use several central nucleotides instead of one, as > in > > alpha <- c(0.1, 0.075, 0.05, 0.03, 0.01, 0.0025, 1e-3, 1e-4); > acc <- AllelicCrosstalkCalibration(csR, alpha=alpha, pairBy="sequence", B=3) > > the number of allele pairs grows quickly: in this particular case > there are 96 allele pairs + 1 missing. > So maybe we it would make sense to hardcode a not to complex layout, > e. g. layout(matrix(seq(length=6, nrow=2))) ? > > Cheers, > > Pierre > >> sessionInfo() > R version 2.8.1 (2008-12-22) > i386-apple-darwin8.11.1 > > locale: > C > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] sfit_0.1.5 aroma.affymetrix_1.0.0 aroma.apd_0.1.3 > [4] R.huge_0.1.6 affxparser_1.14.0 aroma.core_1.0.0 > [7] aroma.light_1.9.2 digest_0.3.1 matrixStats_0.1.3 > [10] R.rsp_0.3.4 R.cache_0.1.7 R.utils_1.1.3 > [13] R.oo_1.4.6 R.methodsS3_1.0.3 > --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
