On Thu, Sep 13, 2012 at 6:11 AM, Reed <ghosh...@gmail.com> 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/
