Dear Henrik, How do I convert illumina BAF, LRR to the bin format.
Please help. Reed On Wednesday, September 12, 2012 8:14:21 PM UTC+5:30, Henrik Bengtsson wrote: > > Hi, > > On Sun, Sep 9, 2012 at 10:18 PM, Unyanee Poolsap > <uny...@gmail.com<javascript:>> > 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-af...@googlegroups.com<javascript:> > > 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/
