hi everyone, im using the function doCRMAv2 but i need to do it setting combineAlleles=FALSE to use the allele specific information for some functions of mine. After applying a correction to the data i want to do CBS, but i cant do it because (im guessing) the alleles have to be summarized, so i dont know how to do this. could anyone help me, please? here is some of my code so you can understand what im doing:
dataSet <- "kotliarov" chipType <- "Mapping50K_Xba240"; dsList <- doCRMAv2(dataSet, chipType=chipType, plm="RmaCnPlm", combineAlleles = FALSE, verbose=-10); print(dsList); # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # CalMaTe - Post-calibration of ASCNs estimates # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - asn <- CalMaTeCalibration(dsList); print(asn); # For speed issues, we will here only process loci on Chromosome 17. dsNList <- process(asn, verbose=verbose); print(dsNList); and now i want to do CBS over the new "dsNList" data, but i dont know how to do it, because if i do cbsModel(dsNList) it gives an error. >sessionInfor(); R version 2.12.2 (2011-02-25) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 LC_MONETARY=Spanish_Spain.1252 [4] LC_NUMERIC=C LC_TIME=Spanish_Spain.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] preprocessCore_1.12.0 DNAcopy_1.24.0 ACNE_0.4.2 MASS_7.3-11 [5] aroma.affymetrix_2.0.0 aroma.apd_0.1.8 affxparser_1.22.1 R.huge_0.2.2 [9] aroma.core_2.0.0 aroma.light_1.18.4 matrixStats_0.2.2 R.rsp_0.4.5 [13] R.cache_0.4.0 R.filesets_0.9.5 digest_0.4.2 R.utils_1.6.5 [17] R.oo_1.7.5 R.methodsS3_1.2.1 loaded via a namespace (and not attached): [1] tools_2.12.2 -- 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/
