Re: QTL analysis

Dear Agus

re:

I am running an animal model with animal, permanent environment and qtl
as random effects for a trait observed only on females. I provide
var(cov)iance matrix for qtl effect with ginv.giv file with the
dimension of 8x8.
The pedigree file (ped.dat) ,for example:
1 0 0
2 0 0
3 0 0
4 1 2
5 3 2
6 1 5
7 3 4
8 1 7

and the data file (tes.dat), for example:
cow sire dam parity hys pe QTL fat <<< I presume the second last column
is the QTL column
4 1 2 1 1 4 4 201
4 1 2 2 3 4 4 280
5 3 2 1 1 5 5 150
5 3 2 2 4 5 5 200
6 1 5 1 2 6 6 160
6 1 5 2 3 6 6 190
7 3 4 1 1 7 7 180
7 3 4 2 3 7 7 250
8 1 7 1 2 8 8 285
8 1 7 2 4 8 8 300

My control file is like this:
Single Trait Genetic Analysis with QTL>>>>>>>>>>>>>
 animal !P
 sire !P
 dam !P
 parity !I
 hys !I
 pe !I
 qtl !P #------------> is this line correct ???? <<< YES
 fat
ped.dat !MAKE
ginv.giv
tes.dat !MAXIT 10

fat ~ mu hys parity !r animal pe qtl

1 1 3
0 0 0

animal 1
animal 0 AINV 3.0

pe 1
pe 0 IDEN 1.5

qtl 1
qtl 0 GIV1 0.5

ASREML run without giving me error message when I put qualifier !P on
the qtl. When I changed into "qtl 8" then I have a warning saying"
Fewer levels found in qtl than specified".
I don't think using !P qualifier for qtl is correct but I have no idea
what is the correct one.

*** In this particular case, either should work equivalently
but I do not expect the specification
 qtl 8
should give a message because 8 is the highest data value.

If in general, the 'pe' column and the 'qtl' columns are the same as the
'cow/animal' column, then 'pe' and 'qtl' columns are not needed.
You would use ide(animal) instead of 'pe' in the model.

This particular model could be simply written (not needing the stuff on
the end) as
   fat ~ mu hys parity !r animal ide(animal) giv(animal,1)
  0 0 0

In general, the !P qualifier is used (for the qtl term) so that
you can be sure the internal coding of the 'qtl' factor corresponds with
the
order used to define the .giv matrix. In particular, using !A or !I
are likely to code the qtl factor in a different order. So if you had
 qtl !I 8
You would get the message you referred to and the coding would be wrong.

Second question is what I should write for the qtl column in my data
file if I assumed only males have been genotyped for marker.

*** The genotyping just changes the IBD matrix, not the data. So the
data file
would not change, just the 'ginv.giv' file.

Grace, mercy and peace to you from God our Saviour Jesus Christ

Arthur Gilmour PhD (see http://www.cargovale.com.au/)
mailto:Arthur.Gilmour_at_dpi.nsw.gov.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

http://www.dpi.nsw.gov.au/reader/17263

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:
Aust Genstat Conf 5-8 Dec Victor Harbour
Leave 18 Dec to 5 Jan
ASReml workshop (Forestry) 16-18 April Tasmania
ASReml workshop (Animal Breeding) May South Africa
AAABG 24-26 September Armidale
      <><><><><><><><><><><><><><><><><><><><><><><><><>

This message is intended for the addressee named and may contain
confidential information. If you are not the intended recipient or
received it in error, please delete the message and notify sender. Views
expressed are those of the individual sender and are not necessarily the
views of their organisation.
Received on Tue Sep 21 2006 - 15:04:42 EST