R中CldList生成的显著性字母与Dunn检验结果不符的求助
2026-6-13
Dunn检验后CldList自动分配显著性字母与手动结果不符的排查需求
问题背景
针对包含季节（Summer、Winter）、位点（Beggers、Noss、Looe）、高度（Low、Mid）的嵌套交互模型，对代谢物特征强度完成成对Dunn检验，检验结果合理。按**共享字母表示无显著差异（p>0.05），无共享字母表示存在显著差异（p<0.05）**的规则，手动为各分组分配了显著性字母。
手动分配的显著性字母
| 分组 | 显著性字母 |
|---|---|
| Winter Looe Mid | B E F G I |
| Summer Beggers Low | A B E |
| Summer Beggers Mid | B E |
| Summer Noss Low | B C H |
| Summer Noss Mid | C |
| Summer Looe Low | C |
| Summer Looe Mid | C |
| Winter Beggers Low | D I |
| Winter Beggers Mid | D E |
| Winter Noss Low | A D F |
| Winter Noss Mid | D G |
| Winter Looe Low | B E F H |
CldList自动分配结果
使用CldList()函数自动分配字母后，结果与手动完全不符，输出如下：
| 序号 | 分组 | 自动分配字母 |
|---|---|---|
| 1 | Summer.Beggers.Low | abcd |
| 2 | Summer.Beggers.Mid | abcd |
| 3 | Summer.Looe.Low | a |
| 4 | Summer.Looe.Mid | a |
| 5 | Summer.Noss.Low | abc |
| 6 | Summer.Noss.Mid | ab |
| 7 | Winter.Beggers.Low | d |
| 8 | Winter.Beggers.Mid | bcd |
| 9 | Winter.Looe.Low | abcd |
| 10 | Winter.Looe.Mid | cd |
| 11 | Winter.Noss.Low | cd |
| 12 | Winter.Noss.Mid | d |
使用的R代码
data$season_site_height_interaction <- interaction(data$season, data$site, data$height) Pyropheo.a.dunn_season_site_height <- dunn.test(data$Pyropheo.a, data$season_site_height_interaction, kw = F, label = TRUE, wrap = TRUE, list=T, altp = TRUE, method = "holm") dunn_df <- data.frame(Comparison = paste(Pyropheo.a.dunn_season_site_height$comparisons), P.adj = Pyropheo.a.dunn_season_site_height$altP.adjusted) dunn_df$Comparison <- gsub("\\s+", " ", dunn_df$Comparison) dunn_df$Comparison <- gsub("^\\s+|\\s+$", "",dunn_df$Comparison) print(head(dunn_df$Comparison)) Pyropheo.a.cld <- cldList(p.value = dunn_df$P.adj,comparison = dunn_df$Comparison,threshold = 0.05) print(Pyropheo.a.cld)
Dunn检验结果表格
| 序号 | 对比分组 | 校正后P值 |
|---|---|---|
| 1 | Summer.Beggers.Low - Summer.Beggers.Mid | 1.000000e+00 |
| 2 | Summer.Beggers.Low - Summer.Looe.Low | 5.330133e-01 |
| 3 | Summer.Beggers.Mid - Summer.Looe.Low | 6.032026e-01 |
| 4 | Summer.Beggers.Low - Summer.Looe.Mid | 4.274224e-01 |
| 5 | Summer.Beggers.Mid - Summer.Looe.Mid | 4.793953e-01 |
| 6 | Summer.Looe.Low - Summer.Looe.Mid | 1.000000e+00 |
| 7 | Summer.Beggers.Low - Summer.Noss.Low | 1.000000e+00 |
| 8 | Summer.Beggers.Mid - Summer.Noss.Low | 1.000000e+00 |
| 9 | Summer.Looe.Low - Summer.Noss.Low | 1.000000e+00 |
| 10 | Summer.Looe.Mid - Summer.Noss.Low | 1.000000e+00 |
| 11 | Summer.Beggers.Low - Summer.Noss.Mid | 1.000000e+00 |
| 12 | Summer.Beggers.Mid - Summer.Noss.Mid | 1.000000e+00 |
| 13 | Summer.Looe.Low - Summer.Noss.Mid | 1.000000e+00 |
| 14 | Summer.Looe.Mid - Summer.Noss.Mid | 1.000000e+00 |
| 15 | Summer.Noss.Low - Summer.Noss.Mid | 1.000000e+00 |
| 16 | Summer.Beggers.Low - Winter.Beggers.Low | 7.406965e-01 |
| 17 | Summer.Beggers.Mid - Winter.Beggers.Low | 6.558980e-01 |
| 18 | Summer.Looe.Low - Winter.Beggers.Low | 1.519886e-04 |
| 19 | Summer.Looe.Mid - Winter.Beggers.Low | 5.850498e-05 |
| 20 | Summer.Noss.Low - Winter.Beggers.Low | 1.443449e-02 |
| 21 | Summer.Noss.Mid - Winter.Beggers.Low | 6.500403e-04 |
| 22 | Summer.Beggers.Low - Winter.Beggers.Mid | 1.000000e+00 |
| 23 | Summer.Beggers.Mid - Winter.Beggers.Mid | 1.000000e+00 |
| 24 | Summer.Looe.Low - Winter.Beggers.Mid | 1.638955e-02 |
| 25 | Summer.Looe.Mid - Winter.Beggers.Mid | 9.319515e-03 |
| 26 | Summer.Noss.Low - Winter.Beggers.Mid | 5.339778e-01 |
| 27 | Summer.Noss.Mid - Winter.Beggers.Mid | 5.745214e-02 |
| 28 | Winter.Beggers.Low - Winter.Beggers.Mid | 1.000000e+00 |
| 29 | Summer.Beggers.Low - Winter.Looe.Low | 9.836811e-01 |
| 30 | Summer.Beggers.Mid - Winter.Looe.Low | 1.000000e+00 |
| 31 | Summer.Looe.Low - Winter.Looe.Low | 6.640483e-01 |
| 32 | Summer.Looe.Mid - Winter.Looe.Low | 5.308907e-01 |
| 33 | Summer.Noss.Low - Winter.Looe.Low | 1.000000e+00 |
| 34 | Summer.Noss.Mid - Winter.Looe.Low | 1.000000e+00 |
| 35 | Winter.Beggers.Low - Winter.Looe.Low | 8.389091e-01 |
| 36 | Winter.Beggers.Mid - Winter.Looe.Low | 1.000000e+00 |
| 37 | Summer.Beggers.Low - Winter.Looe.Mid | 1.000000e+00 |
| 38 | Summer.Beggers.Mid - Winter.Looe.Mid | 1.000000e+00 |
| 39 | Summer.Looe.Low - Winter.Looe.Mid | 1.244590e-02 |
| 40 | Summer.Looe.Mid - Winter.Looe.Mid | 6.777016e-03 |
| 41 | Summer.Noss.Low - Winter.Looe.Mid | 4.409884e-01 |
| 42 | Summer.Noss.Mid - Winter.Looe.Mid | 4.356509e-02 |
| 43 | Winter.Beggers.Low - Winter.Looe.Mid | 1.000000e+00 |
| 44 | Winter.Beggers.Mid - Winter.Looe.Mid | 1.000000e+00 |
| 45 | Winter.Looe.Low - Winter.Looe.Mid | 1.000000e+00 |
| 46 | Summer.Beggers.Low - Winter.Noss.Low | 1.000000e+00 |
| 47 | Summer.Beggers.Mid - Winter.Noss.Low | 1.000000e+00 |
| 48 | Summer.Looe.Low - Winter.Noss.Low | 1.089087e-03 |
| 49 | Summer.Looe.Mid - Winter.Noss.Low | 5.143919e-04 |
| 50 | Summer.Noss.Low - Winter.Noss.Low | 6.109935e-02 |
| 51 | Summer.Noss.Mid - Winter.Noss.Low | 4.241540e-03 |
| 52 | Winter.Beggers.Low - Winter.Noss.Low | 1.000000e+00 |
| 53 | Winter.Beggers.Mid - Winter.Noss.Low | 1.000000e+00 |
| 54 | Winter.Looe.Low - Winter.Noss.Low | 1.000000e+00 |
| 55 | Winter.Looe.Mid - Winter.Noss.Low | 1.000000e+00 |
| 56 | Summer.Beggers.Low - Winter.Noss.Mid | 3.443992e-01 |
| 57 | Summer.Beggers.Mid - Winter.Noss.Mid | 2.974735e-01 |
| 58 | Summer.Looe.Low - Winter.Noss.Mid | 2.646228e-05 |
| 59 | Summer.Looe.Mid - Winter.Noss.Mid | 8.754537e-06 |
| 60 | Summer.Noss.Low - Winter.Noss.Mid | 3.579508e-03 |
| 61 | Summer.Noss.Mid - Winter.Noss.Mid | 1.185647e-04 |
| 62 | Winter.Beggers.Low - Winter.Noss.Mid | 1.000000e+00 |
| 63 | Winter.Beggers.Mid - Winter.Noss.Mid | 1.000000e+00 |
| 64 | Winter.Looe.Low - Winter.Noss.Mid | 4.151544e-01 |
| 65 | Winter.Looe.Mid - Winter.Noss.Mid | 1.000000e+00 |
| 66 | Winter.Noss.Low - Winter.Noss.Mid | 1.000000e+00 |
求助内容
需处理50余种代谢物特征，希望避免手动分配显著性字母的冗余工作，但CldList()输出结果与手动完全不符，恳请帮忙排查问题，或告知是否只能手动完成显著性字母分配。
内容的提问来源于stack exchange，提问作者Graham Sharpe
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