selected output for Tukey's HSD in two-way ANOVA in R

Question

I have a large data set with multiple variable. I need to do two-way-ANOVA and then post-hoc pair-wised multiple comparison using Tukey HSD.

the head of my data for first 25 entry is like this:

> head(my_data2, 25 )
   CellType variable     value
1     Cell1       W1 18.780294
2     Cell1       W1 13.932397
3     Cell1       W1 20.877093
4     Cell1       W1  9.291295
5     Cell1       W1 10.939570
6     Cell1       W1 12.236713
7     Cell1       W1 13.810722
8     Cell1       W1 23.944473
9     Cell1       W1 17.355429
10    Cell1       W1 18.248215
11    Cell2       W1 17.988200
12    Cell2       W1 15.427909
13    Cell2       W1 21.839687
14    Cell2       W1 22.322325
15    Cell2       W1 12.535762
16    Cell2       W1 12.743278
17    Cell2       W1 15.007214
18    Cell2       W1 12.054787
19    Cell2       W1 15.639977
20    Cell2       W1 16.006960
21    Cell3       W1 17.452199
22    Cell3       W1 23.280391
23    Cell3       W1  7.902728
24    Cell3       W1  8.353992
25    Cell3       W1 24.360250

I do ANOVA

#ANOVA
my_data2$CellType <- as.factor(my_data2$CellType)
my_ANOVA = aov(value ~ CellType + variable + CellType:variable, data = my_data2)
summary(my_ANOVA)

And then post hoc

my_posthoc =TukeyHSD(my_ANOVA, which = "CellType:variable") 
my_posthoc

Everything is OK so far, but the output of my posthoc includes all paired-wise comparison which gives a massive our put of more than 2200 row. for example my out put is like this:

> my_posthoc
  Tukey multiple comparisons of means
    95% family-wise confidence level

Fit: aov(formula = value ~ CellType + variable + CellType:variable, data = my_data2)

$`CellType:variable`
                       diff          lwr         upr     p adj
Cell2:W1-Cell1:W1   0.21499 -29.46177884  29.8917588 1.0000000
Cell3:W1-Cell1:W1   0.88234 -28.79442884  30.5591088 1.0000000
Cell4:W1-Cell1:W1   1.24301 -28.43375884  30.9197788 1.0000000
Cell5:W1-Cell1:W1   1.61684 -28.05992884  31.2936088 1.0000000
Cell6:W1-Cell1:W1   0.65009 -29.02667884  30.3268588 1.0000000
Cell7:W1-Cell1:W1   1.08223 -28.59453884  30.7589988 1.0000000
Cell1:W2-Cell1:W1   9.00094 -20.67582884  38.6777088 1.0000000
Cell2:W2-Cell1:W1  27.62765  -2.04911884  57.3044188 0.1249342
Cell3:W2-Cell1:W1  29.40077  -0.27599884  59.0775388 0.0570151
Cell4:W2-Cell1:W1  28.84731  -0.82945884  58.5240788 0.0736530
Cell5:W2-Cell1:W1  42.51407  12.83730116  72.1908388 0.0000144
Cell6:W2-Cell1:W1  30.78610   1.10933116  60.4628688 0.0288235
Cell7:W2-Cell1:W1  27.62966  -2.04710884  57.3064288 0.1248307
Cell1:W3-Cell1:W1  20.95847  -8.71829884  50.6352388 0.7816085
Cell2:W3-Cell1:W1  42.50116  12.82439116  72.1779288 0.0000146
Cell3:W3-Cell1:W1  47.07037  17.39360116  76.7471388 0.0000004
Cell4:W3-Cell1:W1  47.26760  17.59083116  76.9443688 0.0000003
Cell5:W3-Cell1:W1  64.08026  34.40349116  93.7570288 0.0000000
Cell6:W3-Cell1:W1  53.90284  24.22607116  83.5796088 0.0000000

and at the end says:

[ reached getOption("max.print") -- omitted 2290 rows ]

However I'm only interested in comparison within each variable but not between them. as an example for the above output, I only need Cell1:W1-Cell2:W1 . all within same variable w1. or for example Cell6:W3-Cell1:W3. Im not interested in Cell6:W3-Cell6:W1

How can I specify this? Thanks

cuttlefish44 cuttlefish44 · Accepted Answer · 2019-10-11T07:44:27

I took simple honesty way, separating term (rowname) into four parts and filtering them.

library(dplyr); library(tibble); library(purrr)  # OR library(tidyverse)  # EDITED

my_posthoc2 <- my_posthoc %>% 
  pluck("CellType:variablen") %>%             # get element of list
  as_tibble(rownames = "Term") %>%            # convert to tibble
  separate(Term,                              # separate terms by - and :
           into = c("LL", "LR", "RL", "RR"), 
           sep = "-|:", 
           remove = FALSE) 

my_posthoc2 %>% 
  filter(LR == "W1", RR == "W1")  # get Cell1:W1-Cell2:W1

selected output for Tukey's HSD in two-way ANOVA in R

2 Answers