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  ASReml  ~  Models with parents and heterotic groups

Chloe
Posted: Tue Oct 13, 2009 1:30 pm Reply with quote
Joined: 23 Jul 2009 Posts: 19
Dear all,

I'm trying to fit a model with the effect of the environment (fixed), the 2 parents of the inbreeds and their heterotic groups (random).
Here is the command line:

Recolte !BINOMIAL !LOGIT !TOTAL Plantes ~ mu Environnement,
!r GrHet1 -GrHet2 and(GrHet2),
GrHet1.Parent1 - GrHet2.Parent2 and(GrHet2.Parent2)

I'd like to retrieve the effet of the parents (I don't mind if they are Parent1 or Parent2). Of course, one parent corresponds to one heterotic group, so these factors are associated.

However, I don't know how to write the "predict" statment.

what is the good way to write this???

Thank you for answering!
Chloe
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Arthur
Posted: Tue Oct 13, 2009 11:18 pm Reply with quote
Joined: 05 Aug 2008 Posts: 471 Location: Orange, NSW
Dear Chloe,

I am struggling to understand the coding.

I understand that you have progeny from crossing parents representing 2 heterotic groups. E.g.
HG1 has parents A B C
HG2 has parents D E F
and data has columns
Parent1 Parent2
A E
B E
B F
C D
C F
...
However, you coding also has factors GRHet1 and GrHet 2
which I do not understand unless you either have moren than
2 heterotic groups and/or Parent1 and Parent2 refer to
male and female

so that the data looks like

FemP MaleP HGFem HGMale
A D 1 2
D A 2 1
B D 1 2
B E 1 2
F B 2 1
F C 2 1
...

Then HGFem and(HGMale) FemP and(MaleP)

doesn't make sense because
HGFem and(HGMale) is always 1 1

FemP and(MaleP) picks up the general combining (additive) effect
of the parents.

HGFem FemP and(MaleP)

would give n average effect for which HG was the amle parent.

So until I can understand the model better, and then what effects
need to be combined in the PREDICT statement, I can't help you.

_________________
Arthur Gilmour

Retired Principal Research Scientist (Biometrics)
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Chloe
Posted: Wed Oct 14, 2009 7:24 am Reply with quote
Joined: 23 Jul 2009 Posts: 19
Dear Arthur,

Thank your for looking at my problem.

My data look like this:

Recolte Plantes Environnement Parent1 Parent2 GrHet1 GrHet2
20 100 E1 A G 1 4
30 150 E1 A F 1 3
...

This is maize data.
I'd like to analyse the number of harvested plants ("Recolte"), in relation to the number of sowed plants ("Plantes"), in different environments (I have 7 different environments), each plant being the results of the cross between two parents. Each parent belongs to one and only one heterotic group.
I have 845 parents divided in 4 different heterotic groups.

What do you advise to me?

Best regards,
Chloe
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Arthur
Posted: Wed Oct 14, 2009 11:39 am Reply with quote
Joined: 05 Aug 2008 Posts: 471 Location: Orange, NSW
Dear Chloe,

I would write

Recolte !BINOMIAL !LOGIT !TOTAL Plantes ~ mu Environnement,
!r GrHet1 and(GrHet2) Parent1 and Parent2

predict Parent1 !present GrHet1

Issues:
ASReml needs to be tricked into coding GrHet and Parent conformably.
This is easier in ASReml3 where you can use

Parent1 !A 845
Parent2 !AS Parent1
GrHet1 *
GrHet2 *

Again, the predict may not work as you hope if not all 845 parents appear as
Parent1 since ASReml will not be able to work out the link based on
Parent1 and GrHet1 for those parents that do not appear as Parent1.

You may need a second predict statement

predict Parent2 !PRESENT GrHet2

That should get you started at least.


GrHet1.Parent1 - GrHet2.Parent2 and(GrHet2.Parent2)

_________________
Arthur Gilmour

Retired Principal Research Scientist (Biometrics)
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Chloe
Posted: Wed Oct 14, 2009 3:43 pm Reply with quote
Joined: 23 Jul 2009 Posts: 19
Dear Arthur

I tried what you suggested, that is to say:

Parent1 !A 845
Parent2 !AS Parent1
GrHet1 *
GrHet2 *
Plantes 1
Recolte 1
Recolte !BINOMIAL !LOGIT !TOTAL Plantes ~ mu Environnement,
!r GrHet1 and(GrHet2) Parent1 and Parent2 # "and" is like "+" ????
predict Parent1 !present GrHet1
predict Parent2 !present GrHet2

I obtained a R² between predicted and observed value of 0.78.

I expected to get 2 parts in the .pvs file (because of the 2 "predict" statments), but I get only 1 part. Why?

A lot of the predicted values in the .pvs file are the same. I don't know if I should expect that.

Moreover, I compared the .pvs of this model to the .pvs of

Recolte !BINOMIAL !LOGIT !TOTAL Plantes ~ mu Environnement,
!r Parent2 -Parent1 and(Parent1)
predict Parent1
--> Model M0

The results are poorly correlated.

Then I tried

Parent1 !A 845
Parent2 !AS Parent1
GrHet1 *
GrHet2 *
Plantes 1
Recolte 1
Recolte !BINOMIAL !LOGIT !TOTAL Plantes ~ mu Environnement,
!r GrHet1 and(GrHet2) Parent1 and(Parent2)
predict Parent1 !present GrHet1

I obtained a R² between predicted and observed value of 0.71. But the results were more consistent with M0 (whose R² is 0.76).

...
Have a nice day,

Chloe
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Arthur
Posted: Thu Oct 15, 2009 12:18 am Reply with quote
Joined: 05 Aug 2008 Posts: 471 Location: Orange, NSW
Dear Chloe,

OOPS. Sorry.

PREDICT should be

predict Parent1 !present Parent1 GrHet1
predict Parent2 !present Parent2 GrHet2

I can't comment on the models without seeing the variance components
reported.

You should spot check the predictions by manually adding the appropriate
effects from the .sln file. Thats the only way of being sure you know
what you are getting.





On Wed, 2009-10-14 at 16:43 +0100, Chloe wrote:
Quote:
predict Parent1 !present GrHet1
predict Parent2 !present GrHet2

--
Best Wishes,
Arthur Gilmour

Adjunct Professor
School of Computing and Mathematics
Charles Sturt University

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_________________
Arthur Gilmour

Retired Principal Research Scientist (Biometrics)
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Chloe
Posted: Thu Oct 15, 2009 3:42 pm Reply with quote
Joined: 23 Jul 2009 Posts: 19
Dear Arthur,

It has corrected the problem of repeated values in the .pvs file. Thank you.
I provide you the dataset and the .as file defining the 2 models I'd like to compare.

In the .as file, I think the only first predict statment is needed.
And I wonder what is the meaning of the "and" that you added between Parent1 and Parent2.
I am still compulsing the user guide to find the better way to define the second model. I would naturally write:
"!r GrHet1 and(GrHet2) Parent1 and(Parent2)
predict Parent2 !PRESENT GrHet2"
as Parent2 and GrHet2 are the base factor for "GrHet1 and(GrHet2)" and "Parent1 and(Parent2)" respectively, but this predict statment fails.

What is your opinion?

Best regards,

Chloe



MaizeProd.txt
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This is the dataset in .csv format.

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MaizeProd.as
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Chloe
Posted: Fri Oct 23, 2009 1:02 pm Reply with quote
Joined: 23 Jul 2009 Posts: 19
Dear Arthur,

The main problem I have with the following model you proposed is that I 'm not able to compute the predicted values in the .pvs neither in the .yht from the .sln .

Recolte !BINOMIAL !LOGIT !TOTAL Plantes ~ mu Environnement,
!r GrHet1 and(GrHet2) Parent1 and Parent2
predict Parent1 !PRESENT Parent1 GrHet1

What are the effects to sum to get the .pvs file from the .sln?

Thank you,

Chloe
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