tl;dr my segment means look odd https://imgur.com/a/5yOTodf
I'm analysing Illumina CytoSNP 850k data, that has been pre-processed as a (I believe) combination of Genome Studio and BlueFuse.
Confusingly to me, when the distribution of log2 segment means (i.e. the "copy number") are visualised, it's bimodal around 0.
My expectation would be that most segments display, on average, no copy change and a single peak should be evident at ~0 (this is ignoring any smaller peaks that are assumed to be associated with actual CNV).
Is this a problem with the segmentation algorithm that has been used? Would it be prudent to perform the segmentation again, myself?
Thanks for any help! Dom
The plot itself can be found here - https://imgur.com/a/5yOTodf