Hi, I'm trying to use the R Survival analysis on a windows 7 system. The input data format is described at the end of this mail.
1/ I tried to perform a survival analysis including stratified variables using the following formula. cox.xtab_miR=coxph(Surv(time, status) ~ miR + strata(sex,nbligne, age), data=matrix) and obtain the following error message Warning message: In fitter(X, Y, strats, offset, init, control, weights = weights, : Ran out of iterations and did not converge Is this due to the model (error in formula) or is the number of stratified variables fixed? 2/ I wanted to used the predict information to create a survival model based on the same parameter as previously described - (Surv(time, status) ~ miR + strata(sex,nbligne, age) - and than testing it on the predict set of data.. I there any way to do that? Is there any way to plot this? Many thanks for your help. Kind regards / Sandrine Input data > matrix $time [1] 58.14 17.10 14.71 17.43 16.00 7.00 7.50 8.00 8.00 9.85 20.00 9.14 [13] 3.85 5.00 4.00 13.00 15.71 32.00 33.00 8.00 36.00 8.00 42.00 31.43 [25] 29.71 80.00 25.14 40.00 25.14 30.00 12.00 10.71 28.00 4.57 9.00 15.71 [37] 6.85 39.85 6.57 42.00 16.28 14.00 6.71 12.57 65.14 35.28 33.85 52.00 [49] 24.57 32.71 7.28 70.00 7.28 6.71 23.00 10.00 7.14 19.86 55.42 40.28 [61] 21.28 31.14 34.00 44.00 7.28 70.71 7.57 44.85 56.00 21.14 91.71 $status [1] 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 0 1 0 [26] 0 0 1 0 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 0 1 1 1 1 0 [51] 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 $miR [1] 836.12000 458.64000 442.03000 125.47000 2914.44000 [6] 114.53000 8091.10000 2645.75000 3269.46000 1168.67000 [11] 3541.42000 508.79000 177.34000 4705.90000 6677.30000 [16] 4223.73000 787.69265 415.92000 100.57000 10.58000 [21] 42.78000 29.36000 13.47000 1.00000 13.08000 [26] 67.89000 16.09000 49.01000 75.78000 26.36000 [31] 6.36000 31.64173 218.00000 15699.17000 3215.71000 [36] 294.98000 106678.83000 554.79000 198.53000 161.64000 [41] 2481.18283 1093.70000 5496.18000 144.28000 12.50000 [46] 79.49000 45.64000 31.07000 8.12000 15.27000 [51] 15.65780 18.00000 2172.67000 345.35000 3256.34000 [56] 3332.58000 296.32000 7889.62000 936.50000 458.60000 [61] 1212.32000 2762.48000 1047.78000 3193.43000 319.27000 [66] 16.29000 69.31000 84.11000 35.43000 4.98000 [71] 41.75000 $nbligne [1] 1 2 3 3 2 4 2 3 2 3 3 2 3 4 3 2 2 2 2 3 3 3 2 2 NA [26] 2 2 2 3 4 5 2 1 2 2 3 2 2 3 3 3 2 2 1 6 3 2 1 2 2 [51] 1 2 2 2 2 2 2 2 2 2 1 2 2 2 1 2 2 2 2 2 2 $sex [1] 1 2 1 1 1 2 1 2 1 1 1 2 1 1 1 2 2 1 1 1 1 2 2 1 1 [26] 1 1 1 1 1 1 2 1 2 2 1 1 2 2 1 2 1 1 1 1 1 2 1 2 2 [51] 1 1 1 2 1 1 1 1 1 1 2 1 2 1 2 1 1 1 2 2 2 $age [1] 77.00 64.00 50.00 57.00 60.00 53.00 51.00 57.69 53.50 77.37 65.39 78.10 [13] 51.38 73.22 57.33 53.39 44.68 55.94 58.00 47.00 62.00 48.00 55.00 55.00 [25] 56.00 22.00 77.00 56.09 65.63 48.00 61.00 73.99 68.71 47.34 71.60 61.16 [37] 77.94 73.21 66.45 67.69 48.84 70.96 74.43 65.41 64.73 77.87 58.70 65.00 [49] 73.34 75.64 87.86 57.23 60.43 68.27 64.57 51.12 61.91 60.12 84.54 53.99 [61] 33.88 75.95 43.29 67.38 67.80 66.30 52.36 58.81 69.35 80.47 54.38 $predict [1] TRAINING TRAINING TRAINING TRAINING TRAINING TRAINING TRAINING TRAINING [9] TRAINING TRAINING TRAINING PREDICT PREDICT PREDICT PREDICT PREDICT [17] PREDICT PREDICT TRAINING TRAINING TRAINING TRAINING TRAINING TRAINING [25] TRAINING TRAINING TRAINING TRAINING TRAINING PREDICT PREDICT PREDICT [33] PREDICT PREDICT PREDICT PREDICT PREDICT PREDICT PREDICT PREDICT [41] PREDICT PREDICT PREDICT PREDICT PREDICT PREDICT PREDICT PREDICT [49] PREDICT PREDICT PREDICT PREDICT PREDICT PREDICT PREDICT PREDICT [57] PREDICT PREDICT PREDICT PREDICT PREDICT PREDICT PREDICT PREDICT [65] PREDICT PREDICT PREDICT PREDICT PREDICT PREDICT PREDICT Levels: PREDICT TRAINING -- Sandrine Imbeaud INSERM, UMR U-674, IUH Université Paris Descartes Génomique Fonctionnelle des tumeurs solides 27 rue Juliette Dodu F75010 Paris, France TEL: +33 (0)1 53 72 51 98 FAX: +33 (0)1 53 72 51 92 MOBILE: +33 (0)6 12 69 80 29 http://www.inserm-u674.net/ [[alternative HTML version deleted]]
______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.