| Detailed description |
I had:
> names(orkney_imp@phdata)
[1] "id" "sex" "sex0" "Sex" "age" "plate"
[7] "row" "column" "part" "machine" "GP1Raw" "GP2Raw"
[13] "GP3Raw" "GP4Raw" "GP5Raw" "GP6Raw" "GP7Raw" "GP8Raw"
[19] "GP9Raw" "GP10Raw" "GP11Raw" "GP12Raw" "GP13Raw" "GP14Raw"
[25] "GP15Raw" "GP16Raw" "GP17Raw" "GP18Raw" "GP19Raw" "GP20Raw"
[31] "GP21Raw" "GP22Raw" "GP23Raw" "GP24Raw" "TotalArea" "Conc"
[37] "GP1" "GP2" "GP4" "GP5" "GP6" "GP7"
[43] "GP8" "GP9" "GP10" "GP11" "GP12" "GP13"
[49] "GP14" "GP15" "GP16" "GP17" "GP18" "GP19"
[55] "GP20" "GP21" "GP22" "GP23" "GP24" "DP1"
[61] "DP2" "DP3" "DP4" "DP5" "DP6" "DP7"
[67] "DP8" "DP9" "DP10" "DP11" "DP12" "DP13"
[73] "DP14" "DP15" "DP16" "DP17" "DP18" "DP19"
[79] "DP20" "DP21" "DP22" "DP23" "DP24" "DP25"
[85] "DP26" "DP27" "DP28" "DP29" "DP30" "DP31"
[91] "DP32" "DP33" "DP34" "DP35" "DP36" "DP37"
[97] "DP38" "DP39" "DP40" "DP41" "DP42" "DP43"
[103] "DP44" "DP45" "DP46" "DP47" "DP48" "DP49"
[109] "DP50" "DP51" "DP52" "DP53" "DP54"
> i
[1] 37
Error was generated by:
> poly <- polygenic(orkney_imp@phdata[,i] ~ sex + age + plate + part + machine, data = orkney_imp, kinship.matrix = gkin_imp)
LM estimates of fixed parameters:
desmat(Intercept) desmatsex desmatage desmatplate
-1.847502e+00 -2.174026e-17 -3.334917e-19 1.468850e-01
desmatpart desmatmachine
-5.807583e-18 -3.584089e-17
iteration = 0
Step:
[1] 0 0 0 0 0 0 0 0
Parameter:
[1] -1.847502e+00 -2.174026e-17 -3.334917e-19 1.468850e-01 -5.807583e-18
[6] -3.584089e-17 3.000000e-01 2.160984e-32
Function Value
[1] 1.797693e+308
Gradient:
[1] 0 0 0 0 0 0 0 -Inf
Error in nlm(llFUN, p = parsave, y = y, desmat = desmat, relmat = relmat, :
non-finite value supplied by 'nlm'
But:
> poly <- polygenic(GP1 ~ sex + age + plate + part + machine, data = orkney_imp, kinship.matrix = gkin_imp)
...
...
difFGLS:
[1] 1.144640e-12 8.242126e-11 7.493652e-12 1.352104e-11 2.998067e-11
[6] 4.183117e-10
******************************************
*** GOOD convergence indicated by FGLS ***
******************************************
Why simply changing the way of input gave different outcome?? By the way,
> poly <- polygenic(orkney_imp@phdata[,i] ~ sex + age + plate + part + machine, data = orkney_imp, kinship.matrix = gkin_imp)
worked well.
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