Question: CNV data for Urothelial Bladder carcinoma
0
gravatar for arpa530
3.2 years ago by
arpa53010
India
arpa53010 wrote:

Dear all,

Presently I am working on the CNV data analysis of urothelial bladder carcinoma. I have basically downloaded the data from UCSC cancer genome browser. There are five data sets available for CNV study.The genomic matrix is a tab separated file containing the genomic values for each sample for each probe. The matrix are arranged so that the columns are samples and rows are probes. In addition to this there is one such value after the genomic coordinate. I am wondering what is that value? Are they P-value, Z-value or Q-value. I really didn't get that. Please help me to understand this. I have pasted few examples herewith in yellow marks.

Example:

TCGA-HT-A74H-01 chr1 3208470 3746015 . -0.0133
TCGA-HT-A74H-01 chr1 3752621 6231496 . -0.358
TCGA-HT-A74H-01 chr1 6237409 7138986 . 0.007
TCGA-HT-A74H-01 chr1 7139130 7563206 . -0.3678
TCGA-HT-A74H-01 chr1 7563975 46755042 . 0.0016
TCGA-HT-A74H-01 chr1 46757779 48117532 . -0.3615

 

cnv • 1.1k views
ADD COMMENTlink modified 3.1 years ago • written 3.2 years ago by arpa53010
0
gravatar for Sean Davis
3.1 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

They represent log2 ratios of tumor copy number vs. reference.  Two copies in the tumor would be approximately 0, while a one-copy loss would be approximately -1 (if there is no admixture, etc.).

ADD COMMENTlink written 3.1 years ago by Sean Davis25k
0
gravatar for arpa530
3.1 years ago by
arpa53010
India
arpa53010 wrote:

Dear Davis,

Thanks for your response. I have gone though your answer and now I am quite relaxed to get this answer. As it is a log2 ratio that means should I perform normalization the data? Please let me know. I have basically taken the four CNV data set from UCSC cancer genome browser to perform metanalysis.

ADD COMMENTlink written 3.1 years ago by arpa53010

These are not the "raw data".  Instead, these data have already undergone normalization and "segmentation", I suspect.  You'll need to refer to the source of the data for more details.  

ADD REPLYlink written 3.1 years ago by Sean Davis25k
0
gravatar for arpa530
3.1 years ago by
arpa53010
India
arpa53010 wrote:

Dear Davis,

Thanks for your kind response. I will surely do that.

ADD COMMENTlink written 3.1 years ago by arpa53010
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