Question: Copy number differences between groups
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gravatar for neuro3030
23 months ago by
neuro303010
neuro303010 wrote:

Analogous to differential expression with RNA data, is there a statistic or tool to analyze the frequency of copy number alterations between two groups?

I had imagined this to be a Chi-square performed like 20,000 times (each gene) to see if that particular gene is deleted more than one would expect by chance. However, one cannot assume independence of the events since genes are often recurrently deleted together owing to deletion of large regions.

Any suggestions?

differential gistic cna • 593 views
ADD COMMENTlink written 23 months ago by neuro303010

You might want to reference table 1 here and see which flavor you want https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4394692/

ADD REPLYlink written 23 months ago by btsui290

Thanks. I already used TCGA data to run GISTIC, and I now have the thresholds for copy number alterations: -2, -1, 0, 1, 2. I would like to compare the frequency of these for each gene, between two groups. There are about 20,000 genes. How do I determine which genes are more frequently deleted or amplified in group 1 vs group 2?

ADD REPLYlink written 23 months ago by neuro303010
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