I am processing a set of array CGH data using fairly standard tools (limma for background correction and normalization, DNAcopy for segmentation).
Some of my samples look quite different in terms of quality by visual inspection. I have included two examples here. I have two questions:
- Do you know of any tools/ protocols to perform QC on array CGH data?
- In your experience, can sample DNA quality result in the existing local trends of variation present in sample 1 but not sample 2?