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, Sean

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