User:Tara K. Luckau/Notebook/Team ConGen/2011/11/07: Difference between revisions

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* did it... came up with:
* did it... came up with:
:: [[Image:20111107 StructureLnPD.png|500 px]]
:: [[Image:20111107 StructureLnPD.png|600 px]]
* averaging the 3 iterations of each value of K ... K=1 gives most positive Ln P(D) ... :(




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* used [http://genepop.curtin.edu.au/ GenePop on the Web]
* used [http://genepop.curtin.edu.au/ GenePop on the Web]
* ran the following "options":
* ran the following "options":
** Option 1 - Hardy-Weinberg exact test
:: Option 1 - Hardy-Weinberg exact test
:::: sub-option 3 - exact tests
::: sub-option 3 - exact tests
** Option 2 - Linkage disequilibrium
:: Option 2 - Linkage disequilibrium
:::: sub-option 1 - each pair of loci, log likelihood ratio
::: sub-option 1 - each pair of loci, log likelihood ratio
** Option 3 - Population Differentiation
:: Option 3 - Population Differentiation
:::: sub-option 3 - genotypic differentiation for all populations
::: sub-option 3 - genotypic differentiation for all populations
** Option 5 - Basic Information
:: Option 5 - Basic Information
:::: sub-option 1 - basic info (genotypic matrices, number observed/expected homozygoes/heterozygotes, allele frequencies)
::: sub-option 1 - basic info (genotypic matrices, number observed/expected homozygoes/heterozygotes, allele frequencies)
* saved all output to GenePop folder
* saved all output to GenePop folder


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:::: H<sub>o</sub> overall = average of each locus H<sub>o</sub>
:::: H<sub>o</sub> overall = average of each locus H<sub>o</sub>
:::: but don't know how they get an 'overall' for each locus - it's not the average
:::: but don't know how they get an 'overall' for each locus - it's not the average
===Things I learned from chatting with Rulon===
* try FSTAT ... see if that'll give you H<sub>o</sub> straight up




Revision as of 22:49, 7 November 2011

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Structure

  • continued from yesterday ...


Things I learned from chatting with Rulon

  • standard is to run a few iterations of each value of K
  • do NOT unclick "Compute probability of data (for estimating K)" ... this generates the Ln P(D) statistic that is reported in publications
  • can average the Ln P(D) values for each value of K ... the most positive value of Ln P(D) is the K that Structure likes best


  • did it... came up with:
  • averaging the 3 iterations of each value of K ... K=1 gives most positive Ln P(D) ... :(


GENEPOP

Option 1 - Hardy-Weinberg exact test
sub-option 3 - exact tests
Option 2 - Linkage disequilibrium
sub-option 1 - each pair of loci, log likelihood ratio
Option 3 - Population Differentiation
sub-option 3 - genotypic differentiation for all populations
Option 5 - Basic Information
sub-option 1 - basic info (genotypic matrices, number observed/expected homozygoes/heterozygotes, allele frequencies)
  • saved all output to GenePop folder


  • using Riley et al 2006 as framework for which analyses to run
  • they report (in supplement, Table S2) observed and expected heterozygosities for each locus as well as overall
  • where do they get that from GenePop?
    • looks like they gotta calculate it themselves:
Ho = (number observed heterozygotes) / (number observed heterozygotes + number observed homozygotes)
Ho overall = average of each locus Ho
but don't know how they get an 'overall' for each locus - it's not the average


Things I learned from chatting with Rulon

  • try FSTAT ... see if that'll give you Ho straight up



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