Question: q value in MutSigCV analysis
0
gravatar for wenbinm
2.5 years ago by
wenbinm20
USA
wenbinm20 wrote:

Hi there,

I just used MutSigCV to analyze triple negative breast cancer mutation data from COSMIC. The result it gave me shows there is only one gene whose q value is less than 1.

I notice that in "Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature, 517(7536), p.576." they also used MutSigCV to analyze COSMIC data and "only 19 genes has q value less than 1".

So what's the point of using q value if nearly all genes have q value equal to 1?

Thank you all!

sequencing snp mutation genome • 1.1k views
ADD COMMENTlink modified 2.5 years ago by h.mon32k • written 2.5 years ago by wenbinm20
2
gravatar for h.mon
2.5 years ago by
h.mon32k
Brazil
h.mon32k wrote:

So what's the point of using q value if nearly all genes have q value equal to 1?

To avoid getting false positives. You are performing multiple tests (thousands of them, probably), and you expect by chance alone 5% of them will be false positives. q-values corrects for this multiple testing. In general, it is a good practice, but also depends on your aims, as being more strict about false positives also leads to decreased power, i.e., true effects may be deemed statistically non-significant.

Some references:

https://en.wikipedia.org/wiki/False_discovery_rate (has links to several key statistical papers, in case you want to delve on this)

http://www.nonlinear.com/support/progenesis/comet/faq/v2.0/pq-values.aspx

Differential Expression In Rna-Seq Experiment

http://www.biostathandbook.com/multiplecomparisons.html

ADD COMMENTlink written 2.5 years ago by h.mon32k

Thank you for your quick response. It really helps!

ADD REPLYlink written 2.5 years ago by wenbinm20

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted.
Upvote|Bookmark|Accept

ADD REPLYlink written 2.5 years ago by GenoMax95k
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