Bonferroni refers to a method of adjustment for multiple comparisons in which the p value is divided by the number of tests. It is more conservative than many other such methods.

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Fisher's exact test for 3x5 contingency table in R with post-hoc? Consistently with using Fisher or Chi-squared?

I'm struggling with some (relatively simple) stats questions for some work I'm doing in R, and can't seem to find answers online... I have a factorial response variable of habitat type of a species ...
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16 views

Which means difference test to use?

Currently, my data is count data and I am analyzing it in Proc Glimmix in SAS. My data focuses on how many times birds from two treatments performed stand, sit, forage, ect.... So it basically looks ...
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2answers
42 views

Multiple test correction for categorical variables with many levels

I am creating a binary logistic regression model with the inputs as a single categorical variable with 100 levels. My goal is to find which level of the categorical variable is most likely to result ...
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1answer
56 views

Bonferonni correction on multiple Kruskal-Wallis tests

My data consists of 3 groups, and 6 variables. The data are not normal so I want to use non-parametric tests to uncover significance. The first thing I wanted to get your opinion on is, is it ...
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12 views

Bonferroni family of confidence intervals for fitted values from loess method

I did loess nonparametric regression using one predictor and I wanted to build confidence band around my fitted values. I saw the some posts(links below) for this topic and found that an approximation ...
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93 views

Report in ANCOVA: descriptive means or estimated marginal means?

I have conducted an analysis of covariance, ANCOVA, followed by Bonferroni post-hoc tests, on SPSS. I want to report the differences between my groups in text (APA style) and in a corresponding bar ...
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0answers
32 views

How is plot of p-values distribution related to calculation of the false discovery rate?

I'm running t-tests for all combinations of pairwise comparisons of average length of stay for patients among 30 hospitals. My first approach was to use a Bonferroni corrected significance level of ...
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1answer
62 views

p-value correction for multiple t-tests?

My dataset consists of $n$ genes, each of them described by a vector of expression values, $5$ for "healthy" individuals, and $5$ for "unhealthy" individuals. I am going to run $n$ t-tests (one for ...
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1answer
65 views

multiple pair wise nonparametric comparisons

is it possible to perform multiple pair wise nonparametric comparisons (generally using a Mann–Whitney test) and adjust the significance level used for the decision criteria using a Bonferroni-type ...
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61 views

Post-hoc with Bonferroni a correction after ANOVA with repeated measure in SPSS

does somebody know where I can find the t value of post-hoc tests with Bonferroni correction when using SPSS.From what I get so far, I only see p values. Should I add a command in the script? Thank ...
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23 views

Statistical test for Comparing 6 classifiers over 5 datasets

I did the Friedman test to compare 6 classifiers which are tested over 5 datasets. The null hypothesis was rejected so I proceed with the post-hoc Bonferroni. The X classifier is always first on all ...
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0answers
149 views

How to best approach ANOVA with multiple response variables that might be correlated and Bonferroni Correction

I need some help verifying a simple analysis. I have completed a simple two factor experiment of more or less equal sample sizes. Let's assume for the case of this question that the sample sizes are ...
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0answers
9 views

Appropriate correction for tests for determining best of family

I have a sample of $N$ instances of a problem (assumed to be independent samples of an infinite population of instances). To each of these instances I apply $M$ methods, and record how quickly they ...
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5answers
210 views

What's wrong with Bonferroni adjustments

I had read an article has this title "What's wrong with Bonferroni adjustments?" for Thomas V Perneger He summarized saying that Bonferroni adjustment have, at best, limited applications in ...
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2answers
39 views

Is Bonferroni Correction Appropriate for this Analysis?

Suppose I have performed a study wherein I compare a novel intervention (N) against the standard intervention (S). Participants are assigned to N or S randomly, and the study is performed. There are ...
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1answer
25 views

Do I need to do p-value correction after Kendall correlations?

I'm a neuroscientist and I've done some statistics before, but I'm fairly new to corrections of the p-value (like Bonferroni). I've got 2 groups of patients. For each group, I look into 3 areas of ...
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1answer
73 views

How to describe three groups where the means of two groups are significantly different, but neither of the two groups differ from a third group?

I am comparing 3 means from normal distributions using student's test: $\mu{_1}, \mu{_2}, \mu{_3}$ Results are: $\mu{_1} = \mu{_2}, \mu{_2} = \mu{_3}, \mu{_1} \ne \mu{_3} $ If I want to group my ...
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2answers
82 views

Extent of multiple testing correction

A bit of a strange question. In my fourth year biostatistics class today, we were discussing when and when not to use multiple testing correction, and the professor made an offhand comment. He asked ...
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16 views

Follow up comparisons for a repeated measures ANOVA while ignoring some factors

So I have a big data frame with my dependent variable stored in RT and my subject number stored in s. I'm interested in doing within-subject ANOVAs on the means of each subject score per unique ...
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1answer
90 views

Appropriate non-parametric post-hoc test for baseline comparisons?

I want to evaluate several "classifiers" (machine-learning algorithms) with paired samples. I do not want to compare each algorithms' performance to every other (n x m comparison) but only compare the ...
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4answers
609 views

About the Bonferroni correction

I have 50 variables in my dataset. I have correlated each variable against each variable, thus I have $49·50/2 = 1225$ unique correlations when no variable is tested against itself. Now, suppose I ...
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0answers
29 views

Multiple comparisons, multidimensional data, several groups

Could you please help me with such a problem: Let's assume I have multidimensional data that consists of 30 samples and 10 variables. This is a 30x10 matrix. I have three groups of equal size (10 ...
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2answers
95 views

Why is the Bonferroni correction properly used with planned, and not post hoc, contrasts?

The Wikipedia article on Post hoc analysis says "Bonferroni correction (This is properly used with planned, not post hoc, contrasts.)" but does not explain why the Bonferroni correction is properly ...
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1answer
53 views

What is the intuition for dependence assumption in Benjamini and Hochberg (1995)?

For dealing with multiple testing, Benjamini and Hochberg (1995) assume that the tests are independent. Benjamini and Yekutieli (2001) show that (1) the 1995 result also holds under (I think) weaker ...
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1answer
45 views

Using a binomial approach to calculate significance of multiple significance tests

I have 10 data sets with normal distributions and carrying out significance tests on each one. With this many data sets, there is a good chance that some will be significant by chance. I am going to ...
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2answers
656 views

Post-hoc tests for MANOVA: univariate ANOVAs or discriminant analysis?

I am using a MANOVA test to compare nine different dependent variables (from neuropsychological and neuropsychiatric assessment) between three groups. The output shows a significant influence from ...
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1answer
213 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 ...
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1answer
155 views

When should I use FDR or Bonferroni in multiple comparisons?

I have the following situations : (1) Very large number of variables - say 100 variables and 200 samples (observations). Although level of each variable is just 2 or 3 or 4 max. I am doing linear ...
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2answers
32 views

What are correlations among between test statistics in multiple comparison procedures

In the book Multiple Comparisons Using R Bretz et al write that their R package multcomp improves power above other multiple comparison procedures by "accounting for the structural correlations ...
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0answers
23 views

Multiple testing correction when confirming a correlation with an extended dataset

Consider a given dataset on which I performed a set of independent tests on different (non-independent) variables, and obtained several p-values. I estimated the number of independent tests as being ...
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1answer
59 views

Multilevel Modeling and multiple testing

I am interested in working out the correct way to correct for multiple testing in multilevel models for longitudinal data, where I am investing a potential interaction between two predictors. My ...
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1answer
217 views

Does testing for assumptions affect type I error?

I just performed simple simulation. Made two "populations" with different means and the same variance. Since I prepared them I know that they: are normal, differs in location and both have the same ...
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115 views

Multiple Hypothesis testing correction on non-independent data

Consider a vector $X_i$ with $i \in [1,N]$. Let us say that you divide the vector into two $X_{i}'$ with $i \in [1,j]$ and $X_i''$ with $i \in [j+1, N]$ for several $j$; then for each pair of ...
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77 views

Bonferroni-correction after one-way ANOVA

I conducted a one-way ANOVA: I had two groups and tested, if they differ in three different DVs. Since I tested three times, I thought it was wise to go for Bonferroni-correction. But then I got the ...
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31 views

Identifying formulas from MANOVA in a research paper

I need to identify the formulas for computing the group differences with Bonferroni corrections and Cohen's d effect size in the following paper (chart on the top of page 6): Research Paper What ...
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40 views

Mann-Whitney or ANOVA?

I am conducting a randomized vignette survey and would like to know if Mann-Whitney is the best test to use . Participants will be randomized to an identical scenario where a patient deteriorates ...
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3answers
127 views

Joint Confidence Interval

Given the following model: ${\rm Wage}_i=\beta_0+\beta_1 {\rm Married}_i+\beta_2{\rm Female}_i+\beta_3 {\rm Married}_i \times {\rm Female}_i + \varepsilon_i$, I am interested in finding ...
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2answers
2k views

Is the exact value of a 'p-value' meaningless?

I had a discussion with a statistician back in 2009 where he stated that the exact value of a p-value is irrelevant: the only thing that is important is whether it is significant or not. I.e. one ...
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1answer
43 views

Partially orthogonal planned comparisons

I am comparing 8 means and want to set up a planned comparisons, rather than having my Bonferroni adjustment become overly-conservative in a post-hoc. For my groups I need to make a total of 16 ...
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1answer
48 views

Adjusting significance level with for different kinds of tests (chisq, mann whitney etc.) on the same variable

I have conducted a series of tests on a single, dichotomic variable (presence/absence of a personality disorder in a neurological illness) in order to compare several things (i.e. presence of anxiety ...
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0answers
178 views

Controlling for Type 1 Errors: Post-hoc testing on more than 1 ANOVA

I have conducted several repeated-measures ANOVA's with post-hoc testing via Tukey's HSD whenever the omnibus F-test was significant. I'm having some confusion about controlling for type 1 errors when ...
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1answer
542 views

Does one need to adjust for multiple comparisons when using MANOVA?

There are 10 dependent variables and 2 groups. When I wanted to compare 10 dependent variables between two groups, I performed MANOVA. I wonder if there is a multiple comparison problem in that case. ...
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170 views

Bonferroni correction for two different tests on the same dataset

I am having trouble figuring out the correction factor to choose for a Bonferroni correction. Let me explain. I have two datasets, control ($x$) and data from left ($y_1$, affected limb) and right ...
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1answer
64 views

Bonferroni correction for gene functional category enrichment

I have performed a clustering on 20K genes, and I want to understand how coherent resulting clusters are by calculating the significance of the overlap of the clusters with a number of known GO gene ...
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1answer
45 views

what kind of non-parametric test to use?

I collected data on one sample, the DV could be separated into two groups (success yes vs. no) and then I have several IVs with interval scale. I just don't know if to use Wilcoxon or Man-Whitney ...
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2answers
582 views

Why use Bonferroni over Holm-Bonferroni?

I can see why you might not use a more powerful method, such as the Hochberg method, over the Bonferroni correction, as they may have extra assumptions, such as the independence of hypotheses in this ...
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80 views

Multiple Comparisons Correction on Peason's Chi-Squared Tests

I have a dataset consisting of 1000 samples (rows). Each sample consists of 300 categorical data points (columns). The process of generating these data points has a known probability of generating an ...
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0answers
32 views

How to run a Simes test?

I'm looking to set up a Simes test in R. I'm trying to show that a Simes test is conservative with when a positive correlation exists. I know how correct the p-values using the p.adjust function, ...
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107 views

Is Bonferroni correction too liberal for some dependent hypotheses?

I frequently read that Bonferroni correction also works for dependent hypotheses. However, I don't think that is true and I have a counter example. Can somebody please tell me (a) where my mistake is ...
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0answers
21 views

SPSS-independent-sample-t-test [duplicate]

I want to test mean differences between 4(0,1,2,3) groups for 6 different cell-types. In other words, I would have 6 comparisons to do for each cell-type (0-1,0-2,0-3,1-2,1-3,2-3). I have run a ...