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 -~----------~----~----~----~------~----~------~--~---
