I have been doing some paired total copy number analysis in aroma afyymetrix.
The dataset I have is complicated for haf the dataset I have reference samples, 
for the other half I will do an unpiared analysis.
I alos have data from many different tomor types not just one - I do not have 
the sample number of samples from each type of tumor.

My questions are:

When doing a paired analysis - the normal and tumour data have there own 
directories and allelic cross talk calibration, summarization and PCR fragment 
length normlization is all done separately.
Is this tue for the different tumor types as well - should they be treated 
separately for all of tehse stages or can all the tumor types be put into one 
tumour directory.
Also, I am unable to extarct the reference samples that I want after 
normaization to compare to the matching sanmples say in another tumor type.
Segmentation models cannot be fit unless the number of samples match exactly.

Does this mean that I need to do all the stages again for the subsets of 
reference samples that have matching pairs in the other tumor types?

Many thanks


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