Hi Henrik: I am looking at SNP 500K data for cell-lines that was released from GSK. I followed your example CRMA v2. with CBS segmentation without reference samples. It seems that the scale/dynamic range in the plus side (amplification) is compressed compared with similar data from other sources (same CEL file, or same cell-lines). For example, the erbbB/Her2 region (chr 17, ~35 mb) in BT474 cell-line, I got relative copy number ~ 2, which translate to 4 copies. The same region for BT474 from Sanger center (their CEL data) has ~ 15 copies, while NCI cancer genome workbench (same CEL file, not sure what algoruthm) shows ~28 copies.
I realized that many factors could impact copy number calculation, just want to know your thoughts on this. Could it duo to using average as reference? or something specific for your algorithm? Thanks a lot. Han Chang --~--~---------~--~----~------------~-------~--~----~ When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
