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From |
Neil Shephard <nshephard@gmail.com> |

To |
statalist@hsphsun2.harvard.edu |

Subject |
Re: st: Gene-incidence question/simulation |

Date |
Mon, 23 Mar 2009 10:27:00 +0000 |

On Mon, Mar 23, 2009 at 10:15 AM, moleps islon <moleps2@gmail.com> wrote: > Thanks for the statistical input. I truly appreciate this. However > what I've done instead in order to get an estimate is to run a > simulation whereby I select g random patients in my sample and "give > them" the mutation and then do the usual calculations. Sorry, but I see no benefit to this at all. How are you estimating the proportion of your sample to '"give them" the mutation'? The frequency of the allele will be pivotal to calculating the penetrance, and from your code all you've done is pick a random sample of g patients from the total N. This is highly unlikely to reflect the true frequency of the polymorphism in the population, and all you'll have is a range of estimates based on varying genotype frequencies under a dominant model (see comment below). Further your code doesn't seem to be explicitly accounting for any form of genetic other than a dominant one and you may wish to consider recessive, additive and multiplicative (after all, you presumably have no idea about the mode of inheritance). What organism are you looking at and what marker are you considering? If its humans and a SNP, see if you can find the RS# on HapMap where there will (hopefully) be an estimate of the allele frequency from their standard populations. I don't think you can draw any conclusions from the results that you are obtaining here. You really need to genotype your samples for the mutation to estimate the allele frequency, determine the frequency of each genotype in your data set and then you can start deriving the penetrance and joint probability of developing the two phenotypes. Regards Neil -- "The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data." ~ John Tukey (1986), "Sunset salvo". The American Statistician 40(1). Email - nshephard@gmail.com Website - http://slack.ser.man.ac.uk/ Photos - http://www.flickr.com/photos/slackline/ * * For searches and help try: * http://www.stata.com/help.cgi?search * http://www.stata.com/support/statalist/faq * http://www.ats.ucla.edu/stat/stata/

**Follow-Ups**:**Re: st: Gene-incidence question/simulation***From:*moleps islon <moleps2@gmail.com>

**References**:**st: Gene-incidence question/simulation***From:*moleps islon <moleps2@gmail.com>

**Re: st: Gene-incidence question/simulation***From:*Austin Nichols <austinnichols@gmail.com>

**Re: st: Gene-incidence question/simulation***From:*moleps islon <moleps2@gmail.com>

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