3 votes

What does probe number and segmentation mean in copy number variation (CNV) data

The data you posted looks like it was produced by GISTIC, a program commonly used by TCGA to detect copy number changes. Assuming the data really is GISTIC-produced, my understanding is that "...
Slavatron's user avatar
  • 1,010
3 votes

How to compute CNV from TCGA data

Copy number variation (CNV) has traditionally been detected in the wet lab via FISH, fluorescent in-situ hybridization. By combining targeted DNA oligos to fluorescent reporter proteins, a region with ...
aesthete's user avatar
  • 351
2 votes
Accepted

How to compute CNV from TCGA data

The files you're referencing are completely processed files in the SEG format. The basic files are calculated using both germline and somatic CNV, whereas files denoted nocnv are only somatic (the ...
CKM's user avatar
  • 8,109
2 votes
Accepted

Y Chromosome in Ovary Cancer Data

This question was asked more than six years ago. Since then, the dataset in question has been updated. I accessed the OV-US project dataset from the ICGC Data Portal, specifically ...
acvill's user avatar
  • 8,296
1 vote

Open databases for copy number variations similar to TCGA

The ICGC has CNV data for many different cancer types. It has many both restricted and open data sets. The DCC releases page will let you hunt through them - those that are public are easily ...
Jared Andrews's user avatar
1 vote

How do I find samples/patients in TCGA (the cancer genome atlas) that had radiation therapy?

The process is slightly painful but here is how you do it. Go to UCSC Xena, then launch the browser, hit the Visualize tab, pick your cohort of interest, then in the next menu pick phenotype, and ...
Ankur Chakravarthy's user avatar

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