Hi, On Sun, Sep 9, 2012 at 10:18 PM, Unyanee Poolsap <unya...@gmail.com> wrote: > Hello, > > I have a question regarding to TumorBoost. > I have data from Affymetrix (GenomeWideSNP_6) and Illumina (Omni1-Quad) for > the same set of samples. > I want to do normalization of CNV for the data from both platforms > for the purpose of comparison and false positive cut. > > I can follow the vignettes > (http://aroma-project.org/vignettes/tumorboost-highlevel) > for applying TumorBoost on data from Affymetrix. > However, I have no idea how to apply it to the data from Illumina. > I can export BAF, LRR, and other information from Illumina's GenomeStudio in > a text file format, using "Report Wizard". > It seems that TumorBoost requires binary format of BAF and genotype call > (i.e., *.asb and *.acf respectively). > How can I make such binary files from the text file?
Before anything else, have you considered the low-level API to TumorBoost? http://aroma-project.org/vignettes/tumorboost-lowlevel That operates on basic R data types such as vectors and matrices. If you're considering doing parent-specific segmentation, you may also be interested in Paired PSCBS (which does TumorBoost for you). Have a a look at the 'Paired PSCBS' vignette; http://cran.r-project.org/web/packages/PSCBS/ If you're still interested in aroma-level API to TumorBoost, i.e. TumorBoostNormalization, it is possible to create your own *.asb binary data files containing TCN and BAF. You'll then also need to be able to setup UGP annotation data files (for genomic positions). (The *.acf genotype file can be obtained on the fly). However, if you don't really need this, I recommend to hold back on this one, because in the future there may be easier ways to do this. /Henrik > > Thank you. > > -- > 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/
