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Question: how to analyze TCGA CNV data
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gravatar for ycding
2.7 years ago by
ycding10
United States
ycding10 wrote:

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
ADD COMMENTlink modified 21 months ago by spulido990 • written 2.7 years ago by ycding10

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

ADD REPLYlink written 2.7 years ago by Martin Morgan ♦♦ 21k

Hi Martin,

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

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

ADD REPLYlink written 2.7 years ago by ycding10

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

ADD REPLYlink written 2.7 years ago by Martin Morgan ♦♦ 21k

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

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by NS10
0
gravatar for spulido99
21 months ago by
spulido990
spulido990 wrote:

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."

ADD COMMENTlink modified 21 months ago • written 21 months ago by spulido990
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