I am looking to calculate Aneuploidy across a number of tumor samples downloaded from TCGA and ICGC and I had a couple questions regarding the provided copy number data, specifically the segment mean column (which I think is the most relevant data for my cause).
From what I understand from the documentation and previous questions on biostars the values are in Log2 - from this can I read the following into the data?
- A value of 0 should represent CN2
- If so CN2 represents diploidy and variations represent aberrations
- These changes in copy number are a result of the gain or loss of segments of chromosome
I am rather new at CNV work so please let me know if I am completely missing something or barking up the wrong data column.
Thanks for your time, have a great weekend!
Hi Sean, That's very helpful, thank you!
I ended up assuming that segment mean LRR change across longer segments is more likely to signal changes in ploidy whilst shorter segments are more likely to be a result of duplication... For my purposes that assumption seems to be working O.K. though I am keen to experiment to see how accurate it is.