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?? 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.
