Simplifies the access to the differential expression results table
get.results(DEprot.analyses.object, contrast = 1)A data frame.
get.results(DEprot.analyses.object = DEprot::test.toolbox$diff.exp.limma,
contrast = 1)
#> prot.id basemean.log2 log2.mean.FBS log2.mean.6h.DMSO
#> 1 protein.1 18.54165 18.26954 18.81376
#> 2 protein.2 22.76659 22.43601 23.09716
#> 3 protein.3 16.20940 16.57051 15.84830
#> 4 protein.4 21.19592 21.16429 21.22754
#> 5 protein.5 19.30638 19.18238 19.43038
#> 6 protein.6 15.49009 15.63217 15.34802
#> 7 protein.7 17.00778 17.02135 16.99422
#> 8 protein.8 11.87376 12.65016 11.09737
#> 9 protein.9 11.86314 12.14531 11.58097
#> 10 protein.10 12.84557 13.11600 12.57513
#> 11 protein.11 14.22417 14.25200 14.19634
#> 12 protein.12 14.18435 14.40897 13.95974
#> 13 protein.14 18.17955 18.29240 18.06671
#> 14 protein.15 15.15596 15.29837 15.01355
#> 15 protein.16 16.30529 16.39731 16.21326
#> 16 protein.17 13.44074 14.22905 12.65244
#> 17 protein.18 17.70510 17.48411 17.92609
#> 18 protein.19 15.97148 15.95095 15.99202
#> 19 protein.20 19.39488 19.48232 19.30743
#> 20 protein.21 18.47346 18.47229 18.47463
#> 21 protein.22 16.49923 16.49822 16.50023
#> 22 protein.23 15.42045 15.55763 15.28327
#> 23 protein.24 14.96077 15.07249 14.84904
#> 24 protein.25 18.93194 18.66327 19.20061
#> 25 protein.26 17.13383 16.50644 17.76121
#> 26 protein.27 17.49123 17.68725 17.29522
#> 27 protein.28 11.27083 11.12714 11.41453
#> 28 protein.29 16.36207 16.73584 15.98829
#> 29 protein.30 17.36296 17.05715 17.66877
#> 30 protein.31 12.96098 13.30136 12.62060
#> 31 protein.32 13.33568 13.13449 13.53687
#> 32 protein.33 15.43228 15.42325 15.44131
#> 33 protein.34 12.51808 11.64488 13.39128
#> 34 protein.35 14.31653 14.63020 14.00286
#> 35 protein.36 16.00716 16.04804 15.96629
#> 36 protein.37 19.58236 19.50252 19.66220
#> 37 protein.38 16.53489 16.62487 16.44492
#> 38 protein.39 17.04712 17.27062 16.82361
#> 39 protein.40 16.23806 16.25504 16.22108
#> 40 protein.41 16.32023 16.18395 16.45652
#> 41 protein.42 15.59224 15.31647 15.86801
#> 42 protein.43 16.78640 16.57529 16.99751
#> 43 protein.44 14.07177 13.35538 14.78817
#> 44 protein.45 15.83161 16.10207 15.56115
#> 45 protein.46 15.08760 14.95140 15.22380
#> 46 protein.47 11.57676 12.05615 11.09737
#> 47 protein.48 17.49097 18.35534 16.62660
#> 48 protein.49 17.19600 17.46597 16.92602
#> 49 protein.50 15.79326 15.90305 15.68347
#> 50 protein.51 15.31934 15.76659 14.87209
#> log2.Fold_FBS.vs.6h.DMSO p.value padj statistic df
#> 1 -0.544224676 4.427896e-02 0.147596524 -2.24481885 12.07603
#> 2 -0.661148700 7.839601e-04 0.013066002 -4.44777890 12.07603
#> 3 0.722211468 6.356766e-03 0.039729791 3.29441547 12.07603
#> 4 -0.063254105 6.364553e-01 0.757684869 -0.48485487 12.07603
#> 5 -0.247994864 1.784311e-01 0.301313074 -1.42874053 12.07603
#> 6 0.284145196 1.901038e-01 0.306619057 1.38836673 12.07603
#> 7 0.027126811 9.257379e-01 0.964310362 0.09517368 12.07603
#> 8 1.552794212 1.665947e-02 0.075587042 2.77693409 12.07603
#> 9 0.564337613 7.913609e-02 0.180861891 1.91745883 12.07603
#> 10 0.540865019 7.957923e-02 0.180861891 1.91424404 12.07603
#> 11 0.055655604 9.104436e-01 0.964310362 0.11486028 12.07603
#> 12 0.449233938 2.505459e-01 0.357922740 1.20699387 12.07603
#> 13 0.225695196 1.318760e-01 0.263751963 1.61612059 12.07603
#> 14 0.284825720 2.053350e-01 0.311113673 1.33867000 12.07603
#> 15 0.184057322 3.704641e-01 0.487452764 0.93025197 12.07603
#> 16 1.576610596 2.202141e-04 0.005505352 5.19219755 12.07603
#> 17 -0.441985756 6.765273e-02 0.169131816 -2.00713191 12.07603
#> 18 -0.041072472 8.099475e-01 0.934540359 -0.24582308 12.07603
#> 19 0.174882092 1.669414e-01 0.301313074 1.47070658 12.07603
#> 20 -0.002342062 9.897833e-01 0.989977074 -0.01307262 12.07603
#> 21 -0.002006187 9.899771e-01 0.989977074 -0.01282472 12.07603
#> 22 0.274353614 2.049547e-01 0.311113673 1.33987328 12.07603
#> 23 0.223451682 4.844189e-01 0.591137863 0.72136320 12.07603
#> 24 -0.537343331 5.685128e-02 0.152578809 -2.10542667 12.07603
#> 25 -1.254770376 2.565241e-03 0.032065510 -3.78643199 12.07603
#> 26 0.392025553 2.027113e-02 0.077965881 2.67119555 12.07603
#> 27 -0.287390167 1.780118e-01 0.301313074 -1.43023152 12.07603
#> 28 0.747543162 1.814089e-02 0.075587042 2.73106617 12.07603
#> 29 -0.611619251 5.284939e-03 0.039729791 -3.39389710 12.07603
#> 30 0.680761357 1.281858e-01 0.263751963 1.63331631 12.07603
#> 31 -0.402377887 1.708603e-01 0.301313074 -1.45612638 12.07603
#> 32 -0.018062115 9.246432e-01 0.964310362 -0.09658143 12.07603
#> 33 -1.746402464 5.709602e-03 0.039729791 -3.35223060 12.07603
#> 34 0.627342413 5.160509e-02 0.152578809 2.15965994 12.07603
#> 35 0.081753522 8.223955e-01 0.934540359 0.22940250 12.07603
#> 36 -0.159672887 2.939277e-01 0.397199581 -1.09725524 12.07603
#> 37 0.179953720 4.243063e-01 0.543982455 0.82694692 12.07603
#> 38 0.447016255 3.057894e-02 0.109210499 2.44822492 12.07603
#> 39 0.033956247 8.593931e-01 0.954881259 0.18096967 12.07603
#> 40 -0.272567788 1.260893e-01 0.263751963 -1.64327954 12.07603
#> 41 -0.551538280 5.797995e-02 0.152578809 -2.09437530 12.07603
#> 42 -0.422217281 2.143351e-01 0.315198665 -1.31071100 12.07603
#> 43 -1.432789054 3.356138e-03 0.033561382 -3.63978326 12.07603
#> 44 0.540921400 4.847330e-01 0.591137863 0.72083365 12.07603
#> 45 -0.272402734 2.670459e-01 0.370897116 -1.16364168 12.07603
#> 46 0.958783227 1.704892e-02 0.075587042 2.76449747 12.07603
#> 47 1.728739897 8.421089e-05 0.004210544 5.78807316 12.07603
#> 48 0.539953527 5.248375e-02 0.152578809 2.15022528 12.07603
#> 49 0.219577713 1.807878e-01 0.301313074 1.42041489 12.07603
#> 50 0.894501892 1.588347e-02 0.075587042 2.80259432 12.07603
#> diff.status
#> 1 null
#> 2 null
#> 3 null
#> 4 unresponsive
#> 5 null
#> 6 null
#> 7 unresponsive
#> 8 null
#> 9 null
#> 10 null
#> 11 unresponsive
#> 12 null
#> 13 null
#> 14 null
#> 15 null
#> 16 FBS
#> 17 null
#> 18 unresponsive
#> 19 null
#> 20 unresponsive
#> 21 unresponsive
#> 22 null
#> 23 null
#> 24 null
#> 25 6h.DMSO
#> 26 null
#> 27 null
#> 28 null
#> 29 null
#> 30 null
#> 31 null
#> 32 unresponsive
#> 33 6h.DMSO
#> 34 null
#> 35 unresponsive
#> 36 null
#> 37 null
#> 38 null
#> 39 unresponsive
#> 40 null
#> 41 null
#> 42 null
#> 43 6h.DMSO
#> 44 null
#> 45 null
#> 46 null
#> 47 FBS
#> 48 null
#> 49 null
#> 50 null