Hi guys,
I have a question regarding how to calculate raw copy numbers using common 
reference instead of average of all samples of the study. Basically I want 
to use average of HapMap270 samples as reference for all further copy 
number calculations. 
I have a bunch HapMap270 snp6 cel files and I followed Vignette: Estimation 
of total copy numbers using the CRMA v2 method (10K-CytoScanHD) to Step 5 - 
Calculation of raw copy numbers, and generated ceR and saved it as a RData 
file ceR.Rdata.
My first question is, how to use this data for any future copy number 
analysis? My guess is that instead of calculating the ceR from the sample 
set I can just load the ceR.RData file I saved and use it. Right?
My second question is, how to go ahead from there to calculate the relative 
copy numbers for all unit from all samples? The two examples given in the 
Vignette are for one unit from one sample and for a few unit on chromosome 
2 for one sample. What is the function to retrieve all units on all 
chromosomes instead of units <- getUnitsOnChromosome(gi, chromosome=2, 
region=c(81,86)*1e6)? And what is the function to retrieve all samples 
instead of ce <- getFile(cesN, indexOf(cesN, "NA06985"))?
Thanks a lot for the help,

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