Hello everybody,

I am trying to analyse CNV data from TCGA to get a measure of overall CNV per patient.

When I download the Level 3 files taken from the SNP6 array, there is a column in the file called Segment_Mean. (Example at bottom.)

What do the numbers in this column represent?

I think they might be log ratios, but the link below makes me wonder if they are direct estimates of copy number. (In which case it is puzzling that they aren't whole numbers.)

http://www.broadinstitute.org/cancer/software/genepattern/modules/snp6copynumberpipeline

Thanks for any help,

Stephanie

```
Sample    Chromosome    Start    End    Num_Probes    Segment_Mean
BONZE_p_TCGAb56_SNP_1N_GenomeWideSNP_6_E04_666936    1    151040529    153927851    1558    0.2031
BONZE_p_TCGAb56_SNP_1N_GenomeWideSNP_6_E04_666936    1    153928595    153929981    2    -2.0772
BONZE_p_TCGAb56_SNP_1N_GenomeWideSNP_6_E04_666936    1    153933585    164456865    7473    0.1883
```
Those are the log2 ratio of the tumor intensity to the normal intensity. To convert to an absolute cn, use: `(2^seg_mean)*2`