Thanks, Henrik. I have used small chr1 data to test low level API. Can I run the all chromosome's data at one go? In case of preparing a single input datafile for all chromosome, how to take care about the chromosomal position.
Reed. On Thursday, September 13, 2012 9:36:34 PM UTC+5:30, Henrik Bengtsson wrote: > > On Thu, Sep 13, 2012 at 6:11 AM, Reed <ghos...@gmail.com <javascript:>> > wrote: > > Dear Henrik, > > > > How do I convert illumina BAF, LRR to the bin format. > > For me "bin" means "binary". If you use the low-level API there is no > need to create binary files; just read the Illumina BAF (and LRR) data > into memory in, say, a data frame and then pass those values to > normalizeTumorBoost(). > > /Henrik > > > > > 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> > 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 > >> > 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/
