Hi Henrik,

I have paired normal tumor files from chip type Mapping250K_Nsp
I am following two vignettes 
- http://www.aroma-project.org/vignettes/PairedPSCBS-lowlevel/
*Vignette: Paired parent-specific copy-number segmentation*

*Total copy number analysis using CRMA v1 (10K, 100K, 500K)*

I want to get the copy number of each SNP, so I want -

##               NA06985 NA06991 NA06993 NA06994 NA07000 NA07019## 
SNP_A-1938296 -0.0402  0.0391 -0.0518 -0.0414  0.1967  0.0476## SNP_A-4259059  
0.1519 -0.1174  0.2330 -0.1432 -0.2650  0.1086## SNP_A-1939610 -0.4355 -0.3506 
-0.0181  0.0179  0.3192  0.2245

*Calculating raw total copy numbers manually. *This vignette tells us to 
follow vignette *- **Total copy number analysis using CRMA v1 (10K, 100K, 
500K). *In this vignette I am doing the normalizing steps individually. 

My question is - 
Instead of doing correction of allelic crosstalk, quantile normalization, 
and fragment normalization can I just do doCRMAv2 for each pair and get its 
CnChipSizeEffect and then go to the vignette of calculating raw total copy 
numbers manually?

I also want the BAF of these samples and I feel as if I am basically 
repeating normalizing step in order to get these 2 tasks. 

I have some 150 arrays. 


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