Questions tagged [tukey-hsd]

Tukeys Honest Significant Difference (HSD) is a multiple comparison method based on the studentized range distribution.

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25
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4answers
35k views

Is there a nonparametric equivalent of Tukey HSD?

I am using JMP to examine differences in vegetation cover in growth form groups (trees, shrubs, forbs, etc.) before and after three treatments with a control. My sample size is small (n=5) and most of ...
25
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1answer
66k views

Comparing levels of factors after a GLM in R

Here is a little background about my situation: my data refer to the number of prey successfully eaten by a predator. As the number of prey is limited (25 available) in each trial, I had a column "...
21
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1answer
90k views

Bonferroni or Tukey? When does the number of comparisons become large?

Reading Field's Discovering Statistics Using SPSS (3rd Edition) I was struck by a bit about post-hoc tests in ANOVA. For those wanting to control the Type I error rate he suggests Bonferroni or Tukey ...
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2answers
51k views

How can I get a significant overall ANOVA but no significant pairwise differences with Tukey's procedure?

I performed with R an ANOVA and I got significant differences. However when checking which pairs were significantly different using the Tukey's procedure I did not get any of them. How can this be ...
18
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2answers
145k views

How do you write up Tukey post-hoc findings?

What is the proper way to write a Tukey post-hoc result? There are several examples with different results? Say you have North, South, East and West. ...
14
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2answers
100k views

How to obtain the results of a Tukey HSD post-hoc test in a table showing grouped pairs?

I would love to perform a TukeyHSD post-hoc test after my two-way Anova with R, obtaining a table containing the sorted pairs grouped by significant difference. (Sorry about the wording, I'm still new ...
11
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1answer
962 views

Box plot notches vs. Tukey-Kramer interval

The "notch" help document (or original text) from boxplot in 'R' gives the following: If the notches of two plots do not overlap this is ‘strong evidence’ that the two medians differ (Chambers et ...
11
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1answer
13k views

When to correct p-values in multiple comparisons?

I'm afraid that related questions didn't answer mine. We evaluate the performances of >2 classifiers (machine learning). Our Null hypothesis is that performances do not differ. We perform parametric (...
11
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1answer
6k views

Two-sample $t$-test vs Tukey's method

Even if the $F$ statistic in an ANOVA test is significant, we may need to do further testing before drawing conclusions. The most common method for doing this involves the use of a multiple ...
9
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1answer
3k views

How could a Tukey HSD test be more signif then the uncorrected P value of t.test?

I came by the post "Post-hoc Pairwise Comparisons of Two-way ANOVA" (responding to this post), which shows the following: ...
9
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2answers
9k views

Post-hoc test after 2-factor repeated measures ANOVA in R?

I have problems finding a solution regarding how to run a post-hoc test (Tukey HSD) after a 2-factor (both within-subjects) repeated-measures ANOVA in R. For the ANOVA, I've used the aov -function: <...
7
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3answers
16k views

ANOVA results do not match post-hoc Tukey test, how to proceed?

There has been some discussion about why differences exist between factor significance after an ANOVA and no significance in the pairwise comparisons, and it has been very helpful. However, there is ...
7
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1answer
41k views

Interpreting TukeyHSD output in R

I performed a simple ANOVA in R and then generated the following TukeyHSD() comparisons of means: I have a pretty good idea (I think) of what all this means except the 'p adj'. If I'm correct: The ...
6
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1answer
13k views

Are pairwise Wilcoxon tests a valid non-parametric alternative to Tukey's HSD test?

I am trying to identify significant differences between groups from normal and non-normal distributions. When the distribution is normal the workflow is pretty straightforward: ANOVA and after that a ...
6
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1answer
1k views

Is a post-hoc test supposed to be performed on transformed or original data?

This might be a silly question, but I could not find an equivalent one on CrossValidated. I was wondering: if I transform my data in order to meet the assumption of homoscedasticity before running a ...
6
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2answers
196 views

ANOVA: life after rejecting the null hypothesis

I have multiple groups of data (20+ groups) and test the null hypothesis that they have the same mean. How do I proceed after the null hypothesis is rejected? What is the standard method for selecting ...
6
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0answers
1k views

Will Tukey multiple comparison be the same for different types of Sum Of Squares of ANOVA for an unbalanced design

I am working on Two-Way ANOVA for an unbalanced design. Will Tukey multiple comparison be the same for different types (I, II & III) of Sum Of Squares of ANOVA for an unbalanced design. I am ...
5
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3answers
2k views

Meaning of “post hoc” multiple comparisons

My original thought was “post hoc” in a post hoc multiple comparison procedure means that the procedure is taken after an omnibus test (such as ANOVA F test) gives a significant result. But after ...
4
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1answer
6k views

Does the Tukey HSD test correct for multiple comparisons?

After performing an ANOVA and then doing post hoc tests with a Tukey HSD test is it still necessary to correct for multiple pairwise comparisons or is that done already?
4
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3answers
7k views

How to obtain Tukey Table in R?

The R provides a very confusing function for Tukey distribution. The function qtukey needs a nonsensical parameter nmeans which ...
4
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1answer
1k views

Nested mixed effects with lme4

I am trying to analyze data from an experiment using lme4. In the experiment, subjects saw either dark or bright versions of 50 stimuli (between-subjects; fixed effect "brightness"). All subjects saw ...
4
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1answer
3k views

Non-orthogonal planned comparisons: How to correct alpha?

I have a data set containing three groups (A, B, C). Group A and Group B have undergone two different types of training designed to improve the same thing. Group C is my control group with no ...
4
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1answer
5k views

Why do planned comparisons and post-hoc tests differ?

I conducted a three-way independent ANOVA. I manipulated the sound of my stimulus to be 1: congruent (KON), 2: incongruent (INK) and 3: no sound at all (control condition). One of my planned ...
4
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2answers
1k views

Differing p-values car::Anova, anova & post hoc in logistic regression

I am currently working with a logistic model in R and I have a question regarding the p-values that I get from different types of tests. Since I have separation in my data (caused by X) I use the ...
4
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1answer
465 views

LDA, Tukey HSD: little questions from a chemist

As you may know, analytic methods like PCA or LDA are used everywhere in science. In my case, I'm a chemist, and I use it to differentiate molecules. I have 4 different systems (let's call them A, B, ...
3
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2answers
761 views

Are the sample range and sample variance independent when population is normally distributed?

If a population is normally distributed, the sample mean and sample variance are independent. What about the sample range and sample variance? Are they independent too? I am trying to derive ...
3
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2answers
3k views

Can you accept the alternative hypothesis if the global test is significant but the pairwise comparisons are not?

My hypothesis states that "there would be significant differences among a, b, c and d group on the X measure." I used ANOVA to see the group differences which came out to be significant. After that I ...
3
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2answers
5k views

One of my groups (out of 3) doesn't have normal distribution, while a One-way Anova showed unequal variances (using SPSS); what to do?

I have an experiment where I'm testing the effect of a drug on behavior, measured in seconds. My drug group doesn't have normal distribution, probably because of a bimodal pattern: 6 of the 8 are ...
3
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2answers
200 views

Why are there not obvious improvements over Tukey's method?

Is there a book that explains why there aren't better standard techniques than Tukey and ANOVA, for example? For comparison consider for example I read about the null hypothesis one-sample $t$ test ...
3
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1answer
3k views

Equivalent of Tukey test for chi-square?

As a follow up to my previous question, I learned that the chi square test can be used to compare expected and observed frequency distributions. But... Suppose I have the following data table in CSV, ...
3
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2answers
2k views

Interpreting a Tukey - Kramer Confidence Interval Plot

In order to see if any statistically significant differences in the means of 4 particular diets exist, a post-hoc test is conducted i.e. Tukey – Kramer. Could someone please explain to me the plot ...
3
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2answers
435 views

I have significant differences detected in my glmer model summary but not in my mcp (Tukey) multiple comparisons summary. Why?

I am working on a project looking at ant recruitment to bait in the lab. I want to see which baits ('treatment') the ants recruit to more/less and have multiple measurements for each colony over the ...
3
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1answer
665 views

Post hoc test for 1-way Anova with heteroscedasticity

I understand that post-hoc Tukey contrasts are inadequate on a 1-way ANOVA that violates the homoscedastiscity assumption, and that Games Howell or Dunnet contrasts are among the recommended ...
3
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1answer
4k views

Post-hoc tests on linear mixed model give mixed results.‏

I am quite new to R so apologies if I fail to ask properly. I have done a test comparing bat species richness in five habitats as assessed by three methods. I used a linear mixed model in lme4 and got ...
3
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2answers
180 views

Why “Honestly” in Tukey's Honestly Significant Difference (HSD)?

Why is the word "Honestly" in "Tukey's Honestly Significant Difference"? It seems unusual. Most statistical procedures are developed with the intent to give an "honest" answer. Why is that word ...
3
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1answer
4k views

Tukey with interaction and extracting letters in multcomp

I've seen similar questions posted elsewhere with no answer, so I thought I'd put this out into the CrossValidated universe. I am attempting to do a Tukey's post-hoc test on a model that has an ...
3
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1answer
1k views

Interpretting non-contiguous significance letters from Tukey HSD test in the multcomp package? [closed]

I've only ever seen the compact letter display for Tukey's HSD give contiguous letter groupings but like in the following example this package is giving non-contiguous groupings (ie 'cde' is ...
3
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0answers
153 views

How does using Tukey's test correct for multiple comparison problem?

I am curious about the intuition behind the Tukey's HSD. I know that it is designed for post-hoc test(WHEN and HOW part), but I want to know underlying theory that justifies its usage(WHY part). To ...
3
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0answers
179 views

Comparing the mean of several exponentially distributed variables

(Possibly related to Is there a nonparametric equivalent of Tukey HSD?) Given a set of several exponentially distributed variables (representing data which is modeled this way), I'd like to check ...
3
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1answer
121 views

What's the correct method to rank populations?

I want to rank ten or so sources based on their respective error measurements. A few notes on the sources and measurements: The sources do not have the same number of measurements The number of ...
2
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1answer
7k views

Significant ANOVA interaction but non-significant pairwise comparisons [duplicate]

I ran a two-way ANOVA and got a significant interaction. I ran a Tukey.HSD() post-hoc test in R and no pairwise comparisons were significant. Is this an error on my ...
2
votes
2answers
2k views

Post hoc test for Friedman test

I am running a Friedman test for my non-Gaussian data, on MATLAB. However, I am confused about the post hoc test to choose. Two concerns: (1) MATLAB's multcompare ...
2
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1answer
2k views

Which one to choose Type-I, Type-II, or Type-III ANOVA? [duplicate]

I don't understand what the difference is between TypeI and TypeIII? Since my background is not very mathematics, it's very difficult for me to understand this mathematical notation; Type I SS: SS(A) ...
2
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1answer
5k views

Post Hoc Pairwise Comparison of Interaction in Mixed Effects (lmer) Model

I have searched other posts and textbooks and found numerous variations of the pairwise comparisions for my mixed effects model using code from the multicomp ...
2
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1answer
37 views

Are there any situations where ANOVA performs better/is more useful than Tukey's HSD?

In statistics this week we are learning about ANOVA and Tukey's HSD. If ANOVA only tells you whether the differences in the means of the groups are significant, but Tukey's HSD gives you the ...
2
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1answer
251 views

Possible to have insignificance when two groups have non-overlapping 95% CI for Tukey test?

I am comparing three group means (95% CI), as following: A (n=248) B (n=1000) C (n=102) 1.3 (0.6-2.1) 3.9 (3.1-4.7) 2.5 (1.2-3.9) There ...
2
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1answer
2k views

two-way multiple comparisons in R

This is a subset of my dataset: ...
2
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1answer
4k views

What are the (practical) differences between Tukey's HSD and the Dunn-Sidak correction procedures?

I have a data set with three groups, one of which is a control and the other two groups have been administered either a moderate or a high dose of a drug. The data are not normally or log-normally ...
2
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1answer
92 views

How to do Post hoc tests

I have conducted an experiment with 12 conditions (1 baseline). One of the response variables is binary, others 7 point Likert scale. I want to test all other conditions against the baseline (11 ...
2
votes
1answer
704 views

criteria for choosing a post-hoc tests

After eg. ANOVA there are several post-hoc tests out there (e.g. Tukey, Bonferroni, etc.) but what are the criteria for choosing one over the other? If one is more conservative, shouldn't we use it ...