**0**wrote:

I have log R ratios and beta allele frequencies from Affy6 data. I've used the LRR with the R package fastseg to segment the data. The problem is, I need copy number calls and it appears that fastseg just gave me segmentation means for the LRR and fancy plots. Can I use this to estimate copy number integers or do I need to start back at square one with my LRR & BAF using a different package? After segmenting with fastseg, I have ranges, num.mark (integer), seg.mean (numeric), startRow (integer), and endRow(integer). I've looked into PennCNV & cn.mops but I don't know much about them.

Any guidance would be greatly appreciated.

Take a look at seg.mean, is it a lot of nearly two on autosomes, and one on sex-chr for males ?

3.4kSo far I've only gotten to chromosome 1 but here's a summary of seg.mean

484 Celfiles

Min: -161.800

1st Qu.: -9.000

Median: -0.2105

Mean: -0.4894

3rd Qu.: 8.222

Max: 106.300

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