how to analyze CNV "copy number variation" data
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6.6 years ago
mms140130 ▴ 60

Hello,

I'm trying to use copy number variation data in a model so I have for example gene expression data and SNP data for breast cancer, which is one data point for each patient.

the CNV data is different for each patient there are 23 chromosomes and several segment means, I downloaded the file for tumor data

if anyone can just clarify to me how to analyze such data, Thanks.

Sample  Chromosome  Start   End Num_Probes  Segment_Mean
TCGA-3C-AAAU-10A-01D-A41E-01    1   3218610 95674710    53225   0.0055
TCGA-3C-AAAU-10A-01D-A41E-01    1   95676511    95676518    2   -1.6636
TCGA-3C-AAAU-10A-01D-A41E-01    1   95680124    167057183   24886   0.0053
TCGA-3C-AAAU-10A-01D-A41E-01    1   167057495   167059336   3   -1.0999
TCGA-3C-AAAU-10A-01D-A41E-01    1   167059760   181602002   9213    -8.00E-04
TCGA-3C-AAAU-10A-01D-A41E-01    1   181603120   181609567   6   -1.2009
R gene SNP • 2.6k views
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if anyone can just clarify to me how to analyze such data,

"Analyze" is quite broad. It's unclear what you want to do or what the outcome of this analysis should be.

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Hello mms140130!

It appears that your post has been cross-posted to another site: https://support.bioconductor.org/p/97891/

This is typically not recommended as it runs the risk of annoying people in both communities.

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