Hi. On Thu, Aug 27, 2009 at 3:29 AM, Sukhbir Rattan<sukhbir.rat...@gmail.com> wrote: > Yes, I am taking data from RNA gene expression experiment.(from GEO). > > Can someone guide me from where I can collect the CEL files representing DNA > genotyping Experiments.
You will need matched DNA samples, that is, DNA data for the same individuals as your RNA data. Otherwise, you will not get anything useful out of your analysis, because for an random (independent) individual you can basically only assume that the total copy number is two all over (and to make that assumption you won't need any data files). /Henrik > > By > Sukhbir Singh Rattan. > > On Thu, Aug 27, 2009 at 11:15 AM, Henrik Bengtsson <h...@stat.berkeley.edu> > wrote: >> >> On Wed, Aug 26, 2009 at 10:29 PM, Sukhbir >> Rattan<sukhbir.rat...@gmail.com> wrote: >> > Hi Everyone, >> > >> > I have 15 Affymetrix CEL files represent three pH conditions, >> > acidic,basic, >> > neutral. >> > >> > I have to find the copy number for each gene in each condition. >> > >> > Now, how should I start? >> > >> > Firstly, I know to do the normalization by RMA model using affy package >> > and >> > I end up with probe ID and there expression values. >> > >> > Further, what should I do? >> >> It seems like you only have data from RNA gene expression experiments. >> You need CEL files from DNA genotyping experiments to do copy number >> analysis. When you have that, you could try one of the vignettes: >> >> - Total copy number analysis (10K, 100K, 500K) >> - Estimation of total copy numbers using the CRMA v2 method (10K-6.0) >> >> that you find under Pages >> (http://groups.google.com/group/aroma-affymetrix/web/). >> >> /Henrik >> >> > >> > By >> > Sukhbir Singh Rattan. >> > >> > >> > >> > >> > > >> > >> >> > > > > > --~--~---------~--~----~------------~-------~--~----~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
