Hi, except from saying that genotyping is a much harder problem than CN analysis, I'll only comment on the CN questions below. On Wed, Mar 17, 2010 at 9:45 PM, jeremy wilson <jeremy.wilson88 at="" gmail.com=""> wrote: > Thanks for the reply dear Benilton.. [snip] > In my case, how should I do the CNV analysis with only 8 samples. Are > there any other packages or adjustments you can suggest me to > compensate for the small sample size? We also developed the CRMA copy-number methodology such that it is possible to do the preprocessing on a single hybridization. You still need a reliable reference in order to calculate CN ratios. You don't say what your samples are, but if they are paired tumor-normals, you can run CRMAv2 for the tumor and the matched normal and get high-quality tumor-normal CN ratios (you won't get better results if you have more arrays). If you don't have paired data, you might be able to use the robust average of the 8 samples as your reference - again it may depend on what your samples are. Using an external reference (or pool of reference samples) is doable, but you will definitely get better signal-to-noise ratios if you use an internal (same lab) reference. The CRMAv2 method is implemented in the aroma.affymetrix package: http://www.aroma-project.org/ (there you'll also find references to the method) It is even possible to do LOH with small data sets, even better so in paired tumor-normal settings, but we don't have a nice pipeline setup for this yet. /Henrik > > Please let me know > Thank you > > On Wed, Mar 17, 2010 at 12:17 PM, Benilton Carvalho > <beniltoncarvalho at="" gmail.com=""> wrote: >> Hi Jeremy, [snip] >> About the sample size, you need at least 10 samples to use >> crlmm::computeCopynumber. >> >> b >> >> On Wed, Mar 17, 2010 at 4:45 PM, jeremy wilson >> <jeremy.wilson88 at="" gmail.com=""> wrote: >>> Dear all, [snip] >>> One more question: I have only 8 arrays from the same lab and I need >>> to do LOH and copy number analysis. Will the small number of arrays be >>> problematic? >>> >>> Awaiting for your reply, >>> Thank you >>> JW >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >