Compare plant areas across all treatments and genotypes against the reference genotypes
Plate experiment: test experiment for rosettR
We perform ANOVA suitable for multiple comparisons of the area or relative growth rate a each day, \(y\) as
\(y = \beta_{1,i}x + \beta_{2}b + \epsilon\)
where \(x\) is factor encoding each examined combination (\(i\)) of genotype and treatment and \(b\) is a factor encoding the repeats (blocks) in the experiment. We then get statistics assessing the null hypothesis
\(H_{0_{j,k}}: \beta_{1,i} = \beta_{1,j}\) for \(j\) and \(k\) corresponding to samples of the genotype to be tested, versus the designated reference genotype within the same treatment.
Multiple comparisons were performed using the multcomp package. P-values are adjusted for multiple testing.
| comparison | lwr | upr | Estimate | StdError | tvalue | pvalue | mean_left | mean_right | sd_left | sd_right | response |
|---|---|---|---|---|---|---|---|---|---|---|---|
| bar_control_vs_foo_control | -4.2514 | 2.724 | -0.7639 | 1.3236 | -0.577 | 0.9880 | 16.66 | 17.43 | 5.978 | 5.301 | AREA_11 |
| bar_osmotic_vs_foo_osmotic | -5.0652 | 3.477 | -0.7939 | 1.6211 | -0.490 | 0.9949 | 20.72 | 21.51 | 3.126 | 2.811 | AREA_11 |
| baz_control_vs_foo_control | -1.0276 | 6.023 | 2.4976 | 1.3380 | 1.867 | 0.2885 | 19.93 | 17.43 | 6.628 | 5.301 | AREA_11 |
| baz_osmotic_vs_foo_osmotic | -7.8191 | 0.866 | -3.4766 | 1.6481 | -2.109 | 0.1777 | 18.24 | 21.51 | 5.795 | 2.811 | AREA_11 |
| qux_control_vs_foo_control | -2.0092 | 4.966 | 1.4783 | 1.3236 | 1.117 | 0.7912 | 18.91 | 17.43 | 6.394 | 5.301 | AREA_11 |
| qux_osmotic_vs_foo_osmotic | -6.7293 | 1.813 | -2.4580 | 1.6211 | -1.516 | 0.5104 | 19.06 | 21.51 | 3.438 | 2.811 | AREA_11 |
| bar_control_vs_foo_control | -7.9507 | 4.274 | -1.8381 | 2.3203 | -0.792 | 0.9456 | 29.03 | 30.87 | 9.745 | 8.412 | AREA_14 |
| bar_osmotic_vs_foo_osmotic | -9.1505 | 5.822 | -1.6641 | 2.8418 | -0.586 | 0.9871 | 33.16 | 34.83 | 6.420 | 6.062 | AREA_14 |
| baz_control_vs_foo_control | -0.5721 | 11.785 | 5.6066 | 2.3454 | 2.390 | 0.0934 | 36.47 | 30.87 | 11.799 | 8.412 | AREA_14 |
| baz_osmotic_vs_foo_osmotic | -11.7509 | 3.471 | -4.1397 | 2.8892 | -1.433 | 0.5703 | 30.96 | 34.83 | 8.582 | 6.062 | AREA_14 |
| qux_control_vs_foo_control | -3.9290 | 8.296 | 2.1836 | 2.3203 | 0.941 | 0.8882 | 33.05 | 30.87 | 8.752 | 8.412 | AREA_14 |
| qux_osmotic_vs_foo_osmotic | -10.2690 | 4.704 | -2.7826 | 2.8418 | -0.979 | 0.8697 | 32.05 | 34.83 | 7.545 | 6.062 | AREA_14 |
| bar_control_vs_foo_control | -10.6369 | 6.982 | -1.8277 | 3.3435 | -0.547 | 0.9909 | 41.03 | 42.86 | 13.412 | 11.486 | AREA_16 |
| bar_osmotic_vs_foo_osmotic | -12.2967 | 9.281 | -1.5076 | 4.0949 | -0.368 | 0.9989 | 45.06 | 46.56 | 10.044 | 8.888 | AREA_16 |
| baz_control_vs_foo_control | -0.2883 | 17.521 | 8.6161 | 3.3796 | 2.549 | 0.0626 | 51.48 | 42.86 | 16.116 | 11.486 | AREA_16 |
| baz_osmotic_vs_foo_osmotic | -13.2460 | 8.692 | -2.2771 | 4.1632 | -0.547 | 0.9909 | 44.57 | 46.56 | 12.950 | 8.888 | AREA_16 |
| qux_control_vs_foo_control | -4.3495 | 13.269 | 4.4597 | 3.3435 | 1.334 | 0.6423 | 47.32 | 42.86 | 10.808 | 11.486 | AREA_16 |
| qux_osmotic_vs_foo_osmotic | -13.6049 | 7.973 | -2.8158 | 4.0949 | -0.688 | 0.9715 | 43.75 | 46.56 | 10.753 | 8.888 | AREA_16 |
| bar_control_vs_foo_control | -14.3027 | 8.794 | -2.7546 | 4.3832 | -0.628 | 0.9816 | 51.45 | 54.21 | 16.132 | 14.713 | AREA_18 |
| bar_osmotic_vs_foo_osmotic | -16.7853 | 11.502 | -2.6418 | 5.3683 | -0.492 | 0.9947 | 57.15 | 59.79 | 13.933 | 11.980 | AREA_18 |
| baz_control_vs_foo_control | 1.2004 | 24.546 | 12.8733 | 4.4306 | 2.906 | 0.0234 | 67.08 | 54.21 | 20.374 | 14.713 | AREA_18 |
| baz_osmotic_vs_foo_osmotic | -14.8664 | 13.892 | -0.4871 | 5.4578 | -0.089 | 1.0000 | 59.57 | 59.79 | 17.783 | 11.980 | AREA_18 |
| qux_control_vs_foo_control | -5.6701 | 17.426 | 5.8781 | 4.3832 | 1.341 | 0.6371 | 60.08 | 54.21 | 13.124 | 14.713 | AREA_18 |
| qux_osmotic_vs_foo_osmotic | -18.2265 | 10.061 | -4.0830 | 5.3683 | -0.761 | 0.9546 | 55.70 | 59.79 | 13.791 | 11.980 | AREA_18 |
| bar_control_vs_foo_control | -0.0339 | 0.026 | -0.0042 | 0.0113 | -0.368 | 0.9989 | 0.19 | 0.19 | 0.034 | 0.039 | RGR_11.14 |
| bar_osmotic_vs_foo_osmotic | -0.0402 | 0.033 | -0.0037 | 0.0138 | -0.270 | 0.9998 | 0.15 | 0.16 | 0.031 | 0.035 | RGR_11.14 |
| baz_control_vs_foo_control | -0.0223 | 0.038 | 0.0078 | 0.0114 | 0.680 | 0.9730 | 0.20 | 0.19 | 0.029 | 0.039 | RGR_11.14 |
| baz_osmotic_vs_foo_osmotic | -0.0109 | 0.063 | 0.0262 | 0.0141 | 1.859 | 0.2927 | 0.18 | 0.16 | 0.074 | 0.035 | RGR_11.14 |
| qux_control_vs_foo_control | -0.0285 | 0.031 | 0.0013 | 0.0113 | 0.117 | 1.0000 | 0.20 | 0.19 | 0.046 | 0.039 | RGR_11.14 |
| qux_osmotic_vs_foo_osmotic | -0.0261 | 0.047 | 0.0104 | 0.0138 | 0.750 | 0.9574 | 0.17 | 0.16 | 0.043 | 0.035 | RGR_11.14 |
| bar_control_vs_foo_control | -0.0176 | 0.038 | 0.0100 | 0.0105 | 0.954 | 0.8806 | 0.18 | 0.17 | 0.046 | 0.033 | RGR_14.16 |
| bar_osmotic_vs_foo_osmotic | -0.0398 | 0.029 | -0.0054 | 0.0130 | -0.416 | 0.9978 | 0.15 | 0.15 | 0.032 | 0.032 | RGR_14.16 |
| baz_control_vs_foo_control | -0.0194 | 0.036 | 0.0085 | 0.0106 | 0.798 | 0.9429 | 0.17 | 0.17 | 0.045 | 0.033 | RGR_14.16 |
| baz_osmotic_vs_foo_osmotic | -0.0086 | 0.061 | 0.0263 | 0.0133 | 1.982 | 0.2302 | 0.18 | 0.15 | 0.042 | 0.032 | RGR_14.16 |
| qux_control_vs_foo_control | -0.0081 | 0.047 | 0.0195 | 0.0105 | 1.861 | 0.2905 | 0.18 | 0.17 | 0.053 | 0.033 | RGR_14.16 |
| qux_osmotic_vs_foo_osmotic | -0.0354 | 0.033 | -0.0010 | 0.0130 | -0.080 | 1.0000 | 0.15 | 0.15 | 0.018 | 0.032 | RGR_14.16 |
| bar_control_vs_foo_control | -0.0246 | 0.019 | -0.0027 | 0.0083 | -0.326 | 0.9995 | 0.11 | 0.12 | 0.041 | 0.036 | RGR_16.18 |
| bar_osmotic_vs_foo_osmotic | -0.0340 | 0.020 | -0.0072 | 0.0102 | -0.708 | 0.9674 | 0.12 | 0.12 | 0.024 | 0.029 | RGR_16.18 |
| baz_control_vs_foo_control | -0.0052 | 0.039 | 0.0169 | 0.0084 | 2.013 | 0.2174 | 0.13 | 0.12 | 0.037 | 0.036 | RGR_16.18 |
| baz_osmotic_vs_foo_osmotic | -0.0053 | 0.049 | 0.0219 | 0.0103 | 2.118 | 0.1744 | 0.14 | 0.12 | 0.025 | 0.029 | RGR_16.18 |
| qux_control_vs_foo_control | -0.0183 | 0.025 | 0.0036 | 0.0083 | 0.434 | 0.9973 | 0.12 | 0.12 | 0.029 | 0.036 | RGR_16.18 |
| qux_osmotic_vs_foo_osmotic | -0.0303 | 0.023 | -0.0036 | 0.0102 | -0.351 | 0.9992 | 0.12 | 0.12 | 0.018 | 0.029 | RGR_16.18 |
| bar_control_vs_foo_control | -0.0181 | 0.019 | 0.0003 | 0.0070 | 0.043 | 1.0000 | 0.16 | 0.16 | 0.031 | 0.027 | RGR_11.18 |
| bar_osmotic_vs_foo_osmotic | -0.0245 | 0.021 | -0.0020 | 0.0085 | -0.230 | 0.9999 | 0.14 | 0.14 | 0.023 | 0.023 | RGR_11.18 |
| baz_control_vs_foo_control | -0.0080 | 0.029 | 0.0106 | 0.0070 | 1.500 | 0.5221 | 0.17 | 0.16 | 0.023 | 0.027 | RGR_11.18 |
| baz_osmotic_vs_foo_osmotic | 0.0053 | 0.051 | 0.0282 | 0.0087 | 3.248 | 0.0082 | 0.17 | 0.14 | 0.038 | 0.023 | RGR_11.18 |
| qux_control_vs_foo_control | -0.0112 | 0.026 | 0.0072 | 0.0070 | 1.028 | 0.8438 | 0.17 | 0.16 | 0.036 | 0.027 | RGR_11.18 |
| qux_osmotic_vs_foo_osmotic | -0.0161 | 0.029 | 0.0064 | 0.0085 | 0.747 | 0.9582 | 0.15 | 0.14 | 0.021 | 0.023 | RGR_11.18 |
The test results are also given as anova-results.csv
We create effect plots for all comparsions where the mean is indicated by the dot, and the 95% confidence interval indicated by a horizontal line. Red-dots indicate estimates associated with a p-value lower than 0.05.
This report was compiled on Sat Jan 09 20:57:27 2016 by gbfjc on Windows using rosettR v0.0.3