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Hi,
I am running fGWAS for a longitudinal study and I have an issue that I don't know what happened. The number of sample is around 10,000 and the there are 4 observation time points. I got the following error.
obj.phe_EA <- fg.load.phenotype( file.phe.long_EA, file.phe.cov_EA, file.phe.time_EA, file.plot.pdf="/ddn/home2/r2725/projects/jeannette/data/curve.fitting_EA.pdf")
No curve or new curve type is specified, curve fitting is being performed.
Searching curve type ......
Thanks for looking at the error. The problem is very strange. If I choose to get "Power" function for the curve. I can get it run fine. That means it is not about missing data file. Also, if I reduce the number of covariances, it has the same error even it ran fine for the full set. What are the possible causes of the issues if you can tell?
Hi,
I am running fGWAS for a longitudinal study and I have an issue that I don't know what happened. The number of sample is around 10,000 and the there are 4 observation time points. I got the following error.
obj.phe_EA <- fg.load.phenotype( file.phe.long_EA, file.phe.cov_EA, file.phe.time_EA, file.plot.pdf="/ddn/home2/r2725/projects/jeannette/data/curve.fitting_EA.pdf")
No curve or new curve type is specified, curve fitting is being performed.
Searching curve type ......
Curve Fitting Summary:
type parm AIC AICc BIC SSE MSE RMSE R2
1 Logistic 3 8799.088 5.400554 8815.891 162339.75 22.38243 4.731007 -0.1617916
2 Bi-Logistic 6 8794.128 5.398092 8827.733 161452.51 22.26010 4.718061 -0.1554420
3 ABRK 4 7405.987 4.704008 7428.391 80813.23 11.14204 3.337970 0.4216566
4 Pharmacology 3 8799.688 5.400854 8816.491 162388.43 22.38914 4.731716 -0.1621400
5 Exponential 2 8797.698 5.399855 8808.900 162389.27 22.38926 4.731729 -0.1621460
6 Bi-Exponential 4 8800.852 5.401441 8823.256 162320.58 22.37978 4.730728 -0.1616544
7 Power 2 8797.565 5.399788 8808.767 162378.44 22.38776 4.731571 -0.1620685
8 Legendre2 3 8799.634 5.400827 8816.437 162384.06 22.38854 4.731653 -0.1621087
9 Legendre3 4 8801.350 5.401690 8823.753 162360.95 22.38535 4.731316 -0.1619433
10 Legendre4 5 8802.187 5.402114 8830.191 162266.58 22.37234 4.729941 -0.1612679
Curve Type==> ABRK <==
Parameter range estimation ......
Searching covariance matrix .......
*[ 1 / 13 ]: try covariance matrix: AR1
*[ 1 / 13 ]: try covariance matrix: SAD1
*[ 1 / 13 ]: try covariance matrix: ARMA(1,1)
*[ 1 / 13 ]: try covariance matrix: ARH1
*[ 1 / 13 ]: try covariance matrix: CS
*[ 1 / 13 ]: try covariance matrix: CSH
*[ 1 / 13 ]: try covariance matrix: VS
*[ 1 / 13 ]: try covariance matrix: SI
*[ 1 / 13 ]: try covariance matrix: FA1
*[ 1 / 13 ]: try covariance matrix: FAH1
*[ 1 / 13 ]: try covariance matrix: TOEP
*[ 1 / 13 ]: try covariance matrix: TOEPH
*[ 1 / 13 ]: try covariance matrix: HF
Error in fg_dat_est(ret, curve.type, covariance.type, file.plot.pdf, options) :
? No covariance is fitted to this data.
Calls: fg.load.phenotype -> fg_load_phenotype -> fg_dat_est
In addition: There were 42 warnings (use warnings() to see them)
Execution halted
I am wondering if you can help me to find a way to solve that issue? Thank you very much.
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