Hi. On Fri, Sep 14, 2012 at 3:23 AM, Reed <ghosh...@gmail.com> wrote: > 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.
Yes, nothing in the TumorBoost method makes use of genomic locations (nor chromosome or position); it normalizes tumor BAFs given the corresponding matched normal BAFs for SNPs independently of each other. /H > > 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> 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/ -- 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/
