Hi. On Fri, Sep 3, 2010 at 10:38 AM, Kai <wangz...@gmail.com> wrote: > Hi everyone, > > Does anyone know whether the results from "multi-source copy-number > normalization" can be further processed by segmentation model such as > CBS and visualized in ChromosomeExplorer?
First of all, if it is possible to pass a CN data set to CbsModel, GladModel, HaarSegModel etc, then it is basically possible for ChromosomeExplorer process it too. > > There is vignette on MSCN (http://www.aroma-project.org/node/88), > which talks about how to create binary data files containing copy > number estimates from multiple platforms, and smoothed CN estimates. I > was wondering whether these copy number estimates can be used to > generate segmentation by CBS and subsequently visualized by > ChromosomeExplorer. Yes, in the sense that you can process each platform separately, but unfortunately still *no* in the sense that you cannot process them jointly. This is the case both before and after multi-source copy-number normalization (MSCN). A SINGEL PLATFORM: For instance, if you set up a platform-independent data set (*.asb files) as in the 'Multi-source copy-number normalization (MSCN)' vignette [http://aroma-project.org/vignettes/MSCN], e.g. ds <- AromaUnitTotalCnBinarySet$byName(dataSet, tags=tags, chipType="*"); Then you can pass this to CbsModel just as you pass an CnChipEffectSet 'ces' in one of the total CN vignettes, e.g. cbs <- CbsModel(ds); ce <- ChromosomeExplorer(cbs); MULTIPLE PLATFORMS: In case you want to segment MSCN normalized data across multiple platforms, you have to turn to the low-level methods available in aroma. This means that you can not leverage the automatic pipelines of the CbsModel and/or ChromosomeExplorer. You have to do your storing and plotting of results yourself. Here is an outline: Say you have a 'dsList' list object containing AromaUnitTotalCnBinarySet from multiple platforms after MSCN normalization as in http://aroma-project.org/vignettes/MSCN, e.g. library("aroma.cn"); log <- Arguments$getVerbose(-8, timestamp=TRUE); tagsList <- list("MSKCC", "Harvard", "Stanford", "Broad"); dataSet <- "TCGA,GBM,testSet,pairs"; dsList <- lapply(tagsList, FUN=function(tags) { AromaUnitTotalCnBinarySet$byName(dataSet, tags=tags, chipType="*"); }); ugp <- AromaUgpFile$byChipType("GenericHuman", tags="100kb"); mscn <- MultiSourceCopyNumberNormalization(dsList, fitUgp=ugp); dsNList <- process(mscn, verbose=verbose); The you can extract a list of data files for one particular sample across platforms as: dfList <- getFileList(dsList, sampleName); >From this list of files (for the same sample), you can then extract a RawCopyNumbers object contain all the CN data for a particular chromosome as: cn <- extractMergedRawCopyNumbers(dfList, chromosome=chromosome, verbose=verbose); Please note that extractMergedRawCopyNumbers() is a non-documented alpha/beta function, so it may change in the future. Now, with this RawCopyNumbers 'cn' object you can do neat things, e.g. print(cn); plot(cn, pch=".", cex=2, col=cn$id); fit <- segmentByCBS(cn, verbose=verbose); drawCnRegions(fit, lwd=3); str(fit); Feel free to give feedback so we can develop this use case further. Hope this helps. /Henrik > > > Thank you very much. > > Best, > Kai > > -- > 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/
