Hi. On Mon, May 16, 2011 at 9:18 AM, mortiz <mortiz...@gmail.com> wrote: > 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);
An alternative and equivalent wrapper for your convenience/readability is: dsList <- doASCRMAv2(dataSet, chipType=chipType, plm="RmaCnPlm", 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. The 'dsNList' object is of the same kind as the 'dsList', i.e. a list containing two data sets, one holding the total CNs and one holding the corresponding BAFs. For CBS segmentation, you want to use the total CNs only, e.g. seg <- CbsModel(dsNList$total); Finally, you should update to aroma.affymetrix v2.1.0. I also highly recommend that you update to R v2.13.0. Cheers, Henrik > >>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/ > -- 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/
