From: <arthur.gilmour_at_DPI.NSW.GOV.AU>

Date: Thu, 19 Jun 2008 12:43:21 +1000

Date: Thu, 19 Jun 2008 12:43:21 +1000

Dear Peter,

In the typical situation, ASReml expects will will have to invert the

variance structures and it cannot invert

a variance of ZERO. Therefore if you supply an iniutal value of ZERO for

a variance, ASReml will

plug in some other value. However, a covariance of ZERO is allowed

because that does not make the matrix uninvertable.

(If it is too BIG, it will make it negative definite, and for some

particular values make the matrix singular but these

are not immediately obvious and are trapped elsewhere.

In your situation, since there is no information in the data on these two

particular variances,

it does not matter what value is supplied. However, you need to FIX it

(!GFFP) or you will get a singularity

in the AI matrix. ASReml recognises that the value is not needed and does

not use it.

However, it doesn't realize it doesn't need it at the beginning and so

enforces that it not be ZERO.

Changing

1221 0 IDEN

Trait 0 US 0.8250 0.0 0.1E-7 !GUFF

to

1221 0 IDEN

Trait 0 US 0.8250 0.0 0. !GUFF

failed because ASReml ignores (doesn't see; I won't try and explain WHY)

the zero values and so goes looking

for two more parameters on the next line (but that says

3519 0 IDEN

so the initial values are 0.825 3519 0

and it will fall over reading the next line, being now out of step.

If you used the form

1221 0 IDEN

Trait 0 US !GUFF

0.8250 0.0 0.

I expect it would work (and replace the variance of 0. with some positive

number).

I trust this helps.

May Jesus Christ be gracious to you in 2008,

Arthur Gilmour, His servant .

Mixed model regression mapping for QTL detection in experimental crosses.

Computational Statistics and Data Analysis 51:3749-3764 at

http://dx.doi.org/10.1016/j.csda.2006.12.031

Profile:http://www.dpi.nsw.gov.au/research/staff/arthur-gilmour

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Skype: arthur.gilmour

mailto:Arthur.Gilmour_at_dpi.nsw.gov.au, arthur_at_cargovale.com.au

Principal Research Scientist (Biometrics)

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Peter Adam <peter.j.adam_at_GMAIL.COM>

Sent by: ASReml users discussion group <ASREML-L_at_AGRIC.NSW.GOV.AU>

18/06/2008 07:39 PM

Please respond to

ASReml users discussion group <ASREML-L_at_AGRIC.NSW.GOV.AU>

To

ASREML-L_at_AGRIC.NSW.GOV.AU

cc

Subject

R structure in bivariate analysis

Dear Auther and others:

I am working on bivariate analysis using tree (or animal) model

and in a puzzle about the R structure. In my data, trait A was

measured at sites 2-3-4, and trait B was measured at sites 1-3-4.

I would like to fit heterogeneous residual variances for different

sites. I therefore set the covariances to 0 for sites 1 and 2,

and also fix the variances to 0 for the combinations of site and

trait without data.

I first tried the following code:

!PART 1

trait_a trait_b ~ Trait Tr.site !r Tr.site.rep Tr.tree Tr.site.fam

4 2 3

1200 0 IDEN

Trait 0 US 0.1E-7 0.0 0.6748 !GFFU

1221 0 IDEN

Trait 0 US 0.8250 0.0 0.1E-7 !GUFF

3519 0 IDEN

Trait 0 US 0.8242 0.2106 0.5981

3507 0 IDEN

Trait 0 US 0.8286 0.2127 0.6065

......

and it worked as I expected:

Covariance/Variance/Correlation Matrix UnStructured Residual

0.1000E-07 0.000

0.000 0.6741

Covariance/Variance/Correlation Matrix UnStructured Residual

0.8353 0.000

0.000 0.1000E-07

Covariance/Variance/Correlation Matrix UnStructured Residual

0.8245 -0.1306

-0.9180E-01 0.5996

Covariance/Variance/Correlation Matrix UnStructured Residual

0.8289 -0.7723E-01

-0.5487E-01 0.6090

Then I changed the residual variance for trait A at site 1 from

0.1E-7 to 0.0.

!PART 2

trait_a trait_b ~ Trait Tr.site !r Tr.site.rep Tr.tree Tr.site.fam

4 2 3

1200 0 IDEN

Trait 0 US 0.0 0.0 0.6748 !GFFU

1221 0 IDEN

Trait 0 US 0.8250 0.0 0.1E-7 !GUFF

3519 0 IDEN

Trait 0 US 0.8242 0.2106 0.5981

3507 0 IDEN

Trait 0 US 0.8286 0.2127 0.6065

......

I noticed that instead of fixing it to 0, ASReml filled the first

variance with a non-zero value (0.3885):

Covariance/Variance/Correlation Matrix UnStructured Residual

0.3885 0.000

0.000 0.6741

Covariance/Variance/Correlation Matrix UnStructured Residual

0.8353 0.000

0.000 0.1000E-07

Covariance/Variance/Correlation Matrix UnStructured Residual

0.8245 -0.1306

-0.9180E-01 0.5996

Covariance/Variance/Correlation Matrix UnStructured Residual

0.8289 -0.7723E-01

-0.5487E-01 0.6090

I further changed the another 0.1E-7 to 0 as well, and ASReml failed

with the message: "REQUIRE !ASUV qualifier for this R structure". The

error message changed to "Error structures are wrong size" once I used

!ASUV qualifier (and added !f mv in the model as well).

So, how does ASReml treat 0s in R structure? What is the real

difference between 0 and a very small number like 0.1E-7? Why 0s are

ok for covariances but not for variances?

Thanks!

Peter Adam

Received on Sat Jun 19 2008 - 12:43:21 EST

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