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 

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


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.

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