Question

how to analyze TCGA CNV data

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ycding ▴ 10

@ycding-7496

Last seen 3.5 years ago

United States

Dear R people,

I downloaded TCGA CNV data in the following format; I am not familiar with CNV data and want to know how to process and analyze this type of data, for example, how to convert segment mean to copy number, how to add gene IDs for each chromosome region. I have RNA seq data for the same set of samples and want to examine the correlation between mRNA expression and CNV. Can you give me some suggestion for analysis steps and corresponding software packages?

Thank you!

Sample	Chromosome	Start	End	Num_Probes	Segment_Mean
TCGA-HC-8260-11A-01D-2259-01	1	61735	8176626	4058	-0.0157
TCGA-HC-8260-11A-01D-2259-01	1	8182588	8189285	9	-0.9492
TCGA-HC-8260-11A-01D-2259-01	1	8191792	17030245	4730	0.0015
TCGA-HC-8260-11A-01D-2259-01	1	17035220	17114712	33	-0.307
TCGA-HC-8260-11A-01D-2259-01	1	17177045	17260618	58	0.3641

TCGA CNV correlation between mRNA exprssion and CNV • 8.4k views

ADD COMMENT • link updated 8.2 years ago by spulido99 • 0 • written 9.1 years ago by ycding ▴ 10

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Can you edit your question to add the specific location (url / link) where your TCGA copy number data comes from?

ADD REPLY • link 9.1 years ago Martin Morgan 25k

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Hi Martin,

I downloaded from TCGA website, freely publicly available for level3 data.

https://tcga-data.nci.nih.gov/tcga/dataAccessDownload.htm

ADD REPLY • link 9.1 years ago ycding ▴ 10

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Can you please be more specific? Cancer Type? Assay Type? Platform?

ADD REPLY • link 9.1 years ago Martin Morgan 25k

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@ycding have you found how to analyZe CNV files? I have this question, as well.

ADD REPLY • link 9.0 years ago NS ▴ 60

score 0 · Answer 1 · 2016-02-24

Have you tried to download Firehose results ( http://gdac.broadinstitute.org/ )? The analysis of correlation between mrna and cnv is already computed there (e.g. for GBM http://gdac.broadinstitute.org/runs/analyses__2015_08_21/reports/cancer/GBM-TP/Correlate_CopyNumber_vs_mRNA/nozzle.html )

"Gene level (TCGA Level III) expression data and copy number data of the corresponding loci derived by using the CNTools package of Bioconductor were used for the calculations. Pearson correlation coefficients were calculated for each pair of genes shared by the two data sets across all the samples that were common."