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.)
Thanks for any help,
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