Dear all,

I have SNP array data run on three platforms: Affymetrix SNP6 (n=~250) Illumina OmniExpress (fresh frozen DNA) (n=12) Illumina OmniExpress FFPE (n=48)

Since the cancer I work on is comparatively rare, many of our diagnostic samples are available only as paraffin blocks, so the arrival of the OmniExpress arrays which were reported to work with FFPE material was most welcome (just FYI, 40/48 FFPE arrays have passed Illumina's own QC procedures available within GenomeStudio).

What I would like to do is to test for recurrent copy number abnormalities across the three platforms, in a way that minimises platform-dependent bias as much as possible. To aid me in this, I have 6 samples which have been run across all platforms, enabling direct comparison of segmentation algorithms.

I first tried the GLAD segmentation algorithm, but it didn't seem to work too well with the FFPE data, so I am now trying a second approach, whereby I identify a segmentation algorithm that works well with FFPE data, and then apply the same algorithm to the omni express fresh frozen and SNP6 data.

Does anyone have any ideas about the best way to proceed with this? Generally, as you might expect, the FFPE SNP array data seems to have an inherently higher variance than arrays from fresh frozen DNA, so maybe I could control the variance to match the frozen arrays?

Thanks for any comments you may have.