Re: genetic analysis - categorical trait

Dear ASReml users & Arthur Gilmour,

Thanks for your suggestion.

I have tried as what Arthur Gilmour suggested. Since
the third class of color trait contains only 10
records over 2008, I thus merged it into class 2. I
then have 2-class trait now. I have tried univariate
threshold model, it worked well, but not for the
bivariate with body weight.

I uploaded the color.as, color.asr, pedigree file:
ped2006k.prn, and data file: RC200619DRG.csv in
ftp://ftp.dpi.nsw.gov.au/

Could you please take a look and help me?

Have a nice day!

Best regards,
Sang

--- arthur.gilmour_at_DPI.NSW.GOV.AU wrote:

> Dear Sang
>
> re:
>
> I am one of ASReml user and a student at UMB,
> Norway.
> Could you please show me how to estimate
> heritability
> of categorical trait and the genetic correlation
> between this trait with other continuous traits? I
> couldn't find those information in Manual or
> tutorial
> in ASReml guides.
>
>
> the case:
> Fish fillet color: scores: 1,2,3
> Fixed effect: batches, growout period
> Random effect: animal, dam, family
> Continuous traits: body weight
>
> UNFORTUNATELY ASReml cannot fit the model you
> propose as it cannot
> model a multiple threshold process.
>
> It can fit a BIVARIATE analysis of a BINARY trait
> and a NORMAL trait (see
> the enclosed test example binnor.as).
>
> ASReml 3 is in development and can fit a multiple
> threshold (scored)
> trait albiet
> it is a bit untidy at present, but has not been
> extended to Threshld +
> Normal
>
> My strategy for this data would depend on the
> general cell frequencies.
> If all classes have at least 10% then a Normal
> analysis should be
> reasonable.
>
> Maybe as a student, you want to explore a range of
> models and the
> efficiency of various forms
> of analysis. Feel free to contact me for further
> detail.
>
>
> Text of BINNOR.AS follows (The data [binnor.asd] is
> too big to send to the
> list
> but I will put it at
> ftp://asreml:asreml@ftp.dpi.nsw.gov.au if I can.
>
> Lamb data from ARG thesis page 177-8
> record
> CYR GRP 5
> SEX SIRE 18
>
> Score5 # Express as a proportion
> Score4 Scald FootRot
> rand
> binnor.asd !skip 1 !DOPART $4 !ASUV !MAXIT 40
> !DDF $1 !FCON $2 !KADJ $3
> !PART 1
> Score5 !bin !disp ~ SEX GRP !r SIRE .16783
>
> !PART 2
> Score5 ~ SEX GRP !r SIRE .16783
>
> !PART 3
> rand ~ SEX GRP !r SIRE .16783
>
> #
>
---------------------------------------------------------------
> !PART 4 # Binomial + Normal bivariate
> # !ASUV required so that weights are
> correctly used.
> # !disp omitted in this example because
> variance explicitly set
> # GLMM qualifiers only apply to the first
> trait.
> # There is no syntax yet for specyfying
> GLMM qualifiers on
> second trait
>
> Score5 rand !bin ~ Trait.SEX Trait.GRP !r
> Trait.SIRE
> 1 2 1
> 2513
> 2 0 US 1 -.01 0.25
>
> Trait.SIRE 2
> Trait 0 US 0.067 .05 1.20
> SIRE
>
> #
>
---------------------------------------------------------------
> !PART 40
> Score5 rand !bin ~ Trait.SEX Trait.GRP !r
> Trait.SIRE
> 1 2 1
> 2513
> 2 0 US 1 0.00 0.25 !GUFP
>
> Trait.SIRE 2
> Trait 0 US 0.067 .00 1.20 !GUFP
> SIRE
>
> #
>
---------------------------------------------------------------
> !PART 5
> Score5 rand ~ Trait.SEX Trait.GRP !r Trait.SIRE
> 1 2 1
> 2513 !S2==1
> 2 0 US 0.2 .01 0.25
>
> Trait.SIRE 2
> Trait 0 US 0.015 0.01 1.05
> SIRE
>
>
>
>
>
>
> May you know Jesus Christ and His blessing in 2007,
>
> Arthur Gilmour, His servant .
>
> Mixed model regression mapping for QTL detection in
> experimental crosses.
> Computational Statistics and Data Analysis
> 51:3749-3764 now available at
> http://dx.doi.org/10.1016/j.csda.2006.12.031
>
> Profile: http://www.dpi.nsw.gov.au/reader/17263
> Personal website: http://www.cargovale.com.au/
>
> mailto:Arthur.Gilmour_at_dpi.nsw.gov.au,
> arthur_at_cargovale.com.au
> Principal Research Scientist (Biometrics)
> NSW Department of Primary Industries
> Orange Agricultural Institute, Forest Rd, ORANGE,
> 2800, AUSTRALIA
>
> fax: 02 6391 3899; 02 6391 3922
> Australia +61
> telephone work: 02 6391 3815; home: 02 6364 3288;
> mobile: 0438 251 426
>
> ASREML 2 is now available from
> http://www.VSNi.co.uk/products/asreml
> The ASReml discussion group is at
> ASREML-L_at_dpi.nsw.gov.au
> To join it, mailto:arthur.gilmour_at_dpi.nsw.gov.au
> Cookbook: http://uncronopio.org/ASReml
>
> Proposed travel:
> ASReml workshop (Forestry) 16-18 April Tasmania
> Rec leave 19-20 April
> ASReml planning at Tumut 23-27 April
> Biom Brch meet 2-4 May
> ASReml workshop (Animal Breeding) 8-26 May South
> Africa
> AAABG 24-26 September Armidale
>
> <><><><><><><><><><><><><><><><><><><><><><><><><>
>
>
>
>
> nguyen sang <nguyenvansang1973_at_YAHOO.COM>
> Sent by: ASReml users discussion group
> <ASREML-L_at_AGRIC.NSW.GOV.AU>
> 20/04/2007 06:58 PM
> Please respond to ASReml users discussion group
>
>
> To: ASREML-L_at_AGRIC.NSW.GOV.AU
> cc:
> Subject: Re: genetic analysis -
> categorical trait
>
>
> Dear Sir/Madam,
>
> I am one of ASReml user and a student at UMB,
> Norway.
> Could you please show me how to estimate
> heritability
> of categorical trait and the genetic correlation
> between this trait with other continuous traits? I
> couldn't find those information in Manual or
> tutorial
> in ASReml guides.
>
> the case:
> Fish fillet color: scores: 1,2,3
> Fixed effect: batches, growout period
>
=== message truncated ===

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Received on Fri Apr 23 2007 - 13:06:30 EST