TCGA/Broad Institute CNV Files Segment Mean

3

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.)

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

 

 


cnv


tcga

• 11k views

Those are the log2 ratio of the tumor intensity to the normal intensity. To convert to an absolute cn, use:  (2^seg_mean)*2

I have a question , if you please can reply :

to convert BUBBY_p_TCGA_b89_105_SNP_N_GenomeWideSNP_6_D10_777410 > TCGA-2H-A9GF-01A-11D-A37B-01

we have to do it manually before running GISTIC?

thanks

updated 20 months ago by

34k

written 4.3 years ago by

0

I am also wondering how you converted sample ID such as FLOUT_p_TCGAb60_SNP_N_GenomeWideSNP_6_C05_681024 to TCGA barcode ID such as TCGA-2H-A9GF-01A-11D-A37B-01 which is essential for the next analysis. could you please tell your way to solve this? thanks a lot

updated 20 months ago by

34k

written 4.2 years ago by

0


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