Hi. On Mon, Oct 7, 2013 at 4:57 AM, <helping...@gmail.com> wrote: > > Dear aroma members, > > I wish to get your kind opinion regarding an issue. After running CRMAv2 and > performing segmentation (CBS), I would like to run GISTIC analysis. As I > understand I can run GISTIC from the segmented output. However, reading the > GISTIC manual, I found I am required to remove germline CNV before running > GISTIC. > > Therefore I would like to clarify if the workflow below using > aroma.affymetrix is considered accurate since I am NOT using paired-normal? > > The samples I have; > - ~20 Tumour samples > - ~100 Normal/Blood (non-paired) > > Proposed Methods > 1) Run CRMAv2 with ONLY normal/blood > 2) Segment ONLY the normal/blood > 3) Run GISTIC using the segmented data > 4) Identify region considered to be amplified/deleted by GISTIC > > > 5) Run CRMAv2 with ONLY tumour samples > 6) Segment ONLY the tumour samples > 7) Filter out the region identified in 4) as germline CNV > 8) Run GISTIC for the tumour samples > > > The question I would have - Does it make sense to do two separate > segmentation ; A) For normal/blood ONLY ; B) For tumour samples ONLY. And > eventually consider the GISTIC amplified&deleted region in the normal/blood > as germline CNV. > > At this stage I can not see any reasoning why I should NOT run segmentation > for ONLY the normal/blood initialy and consider the regions identified by > GISTIC as germline CNV. > > Perhaps in steps 5-6, should I run CRMAv2 & segmentation with tumour samples > + normal/blood??
I'm not 100% sure what you're exact question is related to aroma.affymetrix/CRMA v2+CBS is, but maybe the following is useful to know: (A) The CRMA v2 method is a truly single-array method, meaning you will get the exact same results from each array regardless if you run them separately or together with other samples. In other words, running CRMA v2 on normal/blood in one batch, and tumors in another gives the exact same estimates as if you run them all together. You can even run them one by one as they come in from the lab. (B) Given that you already have a reference for calculating your CN ratios, the CBS segmentation is also a single-sample method. So, it sounds to me as you need to decided on what reference to use for your CBS segmentation. After that it's all up to GISTIC. /Henrik > > > Any ideas is much appreciated > Zaki > > > -- > -- > 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/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/groups/opt_out. -- -- 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/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out.
