### Sample Discussion

Subject: P-value and Type I error

From drusarkar_at_rediffmail.com Thu Jul 14 09:57:44 2005 Date: 14 Jul 2005 10:16:47 -0000 From: "uttam sarkar" <drusarkar_at_rediffmail.com> Subject: "Help" To: Multiple Recipients of <angenmap_at_animalgenome.org> Dear Sir, My question is: How standard deviation (SD) of gene frequency is estimated for a particular experiment? For example in GH gene Breed N A allele B allele SD Nellore 63 0.91 0.09 ? Thank you. Dr. Uttam Sarkar Ph. D. scholar (AGB) NDRI, India |

From chang_at_calshp.cals.wisc.edu Thu Jul 14 10:15:59 2005 Date: Thu, 14 Jul 2005 10:15:59 -0500 (CDT) From: ruby chang <chang_at_calshp.cals.wisc.edu> Subject: type I error To: Multiple Recipients of <angenmap_at_animalgenome.org> Hi, Type I error (alpha) is usually set at 0.05 level. I find it hard to convince some people that an effect can still be "significant" with a p-value of 0.06. Does anyone know when and where this magic number 0.05 started? Thanks. Ruby Chang Dairy Science Department University of Wisconsin, Madison |

From DNADave_at_U.Arizona.Edu Thu Jul 14 10:28:59 2005 Delivered-To: angenmap_at_genome.ansci.iastate.edu Subject: Re: type I error From: David Henderson <DNADave_at_U.Arizona.Edu> Organization: The University of Arizona Date: Thu, 14 Jul 2005 08:28:35 -0700 To: Multiple Recipients of <angenmap_at_animalgenome.org> > Type I error (alpha) is usually set at 0.05 level. I find it hard > to convince some people that an effect can still be "significant" with a > p-value of 0.06. You are correct. If you take a Neyman-Pearson view of statistics and you want to control your Type I error rate at 5% (for a single test), then you reject only when p < 0.05. If you take the view that Fisher intended, then p-values are only measures of risk whereby p = 0.06 is slightly more risky than p = 0.05, but both could equally be significant in the eye of the right beholder... > Does anyone know when and where this magic number 0.05 started? R.A. Fisher somewhere around 1920. A good read on this is "The Lady Tasting Tea" which describes the story around 0.05 becoming a standard. A famous quote by Fisher is "Surely God loves the 0.06 as much as the 0.05.". Good Luck!! Dave H -- David A. Henderson, Ph.D. Insightful Corporation 1700 Westlake Avenue North, Suite 500 Seattle, WA 98109-3044 Tel: 206-802-2307 Fax: 206-283-8691 DNADave_at_Insightful.Com |

From david.machugh_at_ucd.ie Thu Jul 14 11:23:53 2005 Date: Thu, 14 Jul 2005 17:05:38 +0100 From: David MacHugh <david.machugh_at_ucd.ie> Subject: RE: "Help" To: Multiple Recipients of <angenmap_at_animalgenome.org> Hello Uttam, The variance of an allele frequency estimate is (from the binomial distribution): p(1-p)/2n Where n = the number of animals sampled (half the number of chromosomes assayed for a diploid marker). The SD can be calculated as the square root of this. In your case the variance for both allele frequency estimates would be: 0.91(0.09)/126 = 0.00065 The SD would be then be the square root of 0.00065 = 0.0255 Note, the formula is exactly the same if you have more than two alleles (as is the case for most microsatellites). Hope this helps, David. David MacHugh, Ph.D. SFI Investigator, Animal Genomics Laboratory, School of Agriculture, Food Science and Veterinary Medicine, and Conway Institute for Biomolecular and Biomedical Research, College of Life Sciences, University College Dublin, Belfield, Dublin 4. Ireland. Phone: 353-1-716-7738 Mobile: 353-87-202-9763 Fax: 353-1-716-1103 Email: david.machugh_at_ucd.ie Website: http://www.ucd.ie/ascience/html/dmachugh-frame.html Conway website: http://www.ucd.ie/~conway/ |

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