Dear all,
I'm trying to fit the following function
slope_pp3_mrna = ( (k3 * v3_K_d *p1^v3_h) / ( (v3_Kd^v3_h) + p2^v3_h ) ) *
( 1/(1 + (p2/v4_Kd)^v4_h) ) - pp3_mrna
to this experimental data in the datafraeme "Data_pp3_mrna" (see it at the
end of this e-mail)
I'm using the nls function in the following code. IN the last step of the
fit "fm_pp3_mrna_4", when I add to the funziont the paramter v4_Kd something
goes wrong, and I reeive this message
Error in numericDeriv(form[[3L]], names(ind), env) :
Missing value or an infinity produced when evaluating the model
What could be the error? I tried with differnet intial values of v4_Kd, but
I did not fix the problem.
Here below the code. Thanks in advance,
Paola.
Data_pp3_mrna <- data.frame(
p1 = protein_1,
p2 = protein_2,
pp3_mrna = protein_3_mrna,
slope_pp3_mrna = stinemanSlopes(times,
protein_3_mrna)
)
one_par <- nls(slope_pp3_mrna ~ ( (k3 * p1) / ( (1) + p1 ) ) *
( 1/(1 + (p2)) ) - pp3_mrna,
data=Data_pp3_mrna,
start=list(
k3=0.1
))
summary(one_par)
fm_pp3_mrna_1 <- nls(slope_pp3_mrna ~ ((k3 * v3_Kd *p1) / ( (v3_Kd) + p1 ) )
*
( 1/(1 + (p2)) ) - pp3_mrna,
data=Data_pp3_mrna,
start=list(k3=24,
v3_Kd=1
))
summary(fm_pp3_mrna_1)
fm_pp3_mrna_2 <- nls(slope_pp3_mrna ~ ((k3 * v3_Kd *p1^v3_h) / (
(v3_Kd)^v3_h + p1^v3_h ) ) *
( 1/(1 + (p2)) ) - pp3_mrna,
control = list(maxiter = 500),
data=Data_pp3_mrna,
start=list(k3=69,
v3_Kd=0.3238,
v3_h=1
))
summary(fm_pp3_mrna_2)
fm_pp3_mrna_3 <- nls(slope_pp3_mrna ~ ((k3 * v3_Kd *p1^v3_h) / (
(v3_Kd)^v3_h + p1^v3_h ) ) *
( 1/(1 + (p2)^v4_h) ) - pp3_mrna,
control = list(maxiter = 500),
data=Data_pp3_mrna,
start=list(k3=37.451,
v3_Kd=0.59,
v3_h=2.013,
v4_h=0.000001
))
summary(fm_pp3_mrna_3)
fm_pp3_mrna_4 <- nls(slope_pp3_mrna ~ ((k3 * v3_Kd *p1^v3_h) / (
(v3_Kd)^v3_h + p1^v3_h ) ) *
( 1/(1 + (p2/v4_Kd)^v4_h) ) - pp3_mrna,
control = list(maxiter = 500),
data=Data_pp3_mrna,
start=list(k3=56.2823,
v3_Kd=0.3366,
v3_h=1.8040,
v4_Kd=0.03,
v4_h=0.7693
))
Here the data.
> Data_pp3_mrna
p1 p2 pp3_mrna slope_pp3_mrna
1 1.006 0.921 0.0410000 8.63741887
2 2.235 2.047 2.9069031 2.82619343
3 3.744 3.937 4.0520000 0.84354113
4 4.222 9.340 4.3237353 0.47577213
5 9.022 14.609 4.5310000 -0.03940131
6 11.326 22.765 3.5100000 -2.04200000
7 6.899 17.852 2.4890000 -1.86822481
8 10.709 27.777 1.6222048 -1.55625973
9 14.084 27.785 0.9110000 -0.48800514
10 14.922 23.613 0.8260000 -0.17000000
11 14.340 18.422 0.7410000 -0.22560156
12 13.066 24.085 0.5990000 -0.28400000
13 17.553 18.594 0.4570000 -0.13847372
14 14.803 16.831 0.4550965 0.03588624
15 11.945 14.495 0.4930000 0.09536674
16 11.427 12.458 0.5505361 0.15549062
17 11.556 9.082 0.6490000 0.49638596
18 20.107 9.987 1.2486525 1.36871828
19 15.999 10.305 2.0590000 1.87868197
20 16.094 5.793 3.2285000 2.33900000
21 11.752 6.944 4.3980000 0.80395869
22 15.841 5.575 4.6510000 0.50600000
23 12.601 5.221 4.9040000 0.80270128
24 13.598 2.872 5.8190000 1.83000000
25 13.879 2.883 6.7340000 -0.03571884
26 16.270 2.213 6.4135000 -0.64100000
27 17.176 3.381 6.0930000 -0.33913760
28 12.332 2.781 6.0320000 -0.12200000
29 12.373 3.073 5.9710000 -0.41224459
30 14.781 2.948 5.4890000 -0.96400000
31 17.578 3.953 5.0070000 -0.68258311
32 18.865 2.279 4.7568901 -0.39425557
33 14.735 2.806 4.6060000 0.13264481
34 16.160 1.676 4.9870000 0.76200000
35 13.416 2.478 5.3680000 0.63914248
36 13.864 1.394 5.6374239 0.45419096
37 16.219 2.299 5.8270000 -0.12540453
38 13.249 1.457 5.2505000 -1.15300000
39 14.445 2.325 4.6740000 -0.09880849
40 13.210 2.230 5.5576966 2.17200142
41 12.358 2.116 8.9470000 11.38521228
--
*Paola Lecca, PhD*
*The Microsoft Research - University of Trento*
*Centre for Computational and Systems Biology*
*Piazza Manci 17 38123 Povo/Trento, Italy*
*Phome: +39 0461282843*
*Fax: +39 0461282814*
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