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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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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19 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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100 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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8 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
162 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
35 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
50 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
69 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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10 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
60 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
555 views

About the Bonferroni correction

I have 50 variables in my dataset. I have correlated each variable against each variable, thus I have $49ยท50/2 = 1225$ unique correlations when no variable is tested against itself. Now, suppose I ...
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25 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
69 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
45 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
43 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
175 views

Post-hoc tests for MANOVA

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
126 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
99 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
30 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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19 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
42 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
196 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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107 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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68 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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30 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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35 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
96 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
42 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
47 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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159 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
354 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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135 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
48 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
41 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
443 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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72 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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29 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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84 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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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 ...
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2answers
73 views

How to compare several small groups with follow-up data?

I have 4 treatment groups: 1 control (placebo) 1 with X treatment 1 with Y treatment 1 combination-treatment-group XY and I have monitored the individuals ...
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88 views

Bonferroni Multiple comparisons — testing for any true

I am doing multiple comparisons with several thousand independent alternatives. None are statistically significant when Bonferroni corrected; however, many more are significant when uncorrected than ...
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104 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 ...
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1answer
1k views

How and when to use the Bonferroni adjustment

I have two questions regarding when to use a Bonferroni adjustment: Is it appropriate to use a Bonferroni adjustment in all cases of multiple testing? If one performs a test on a data set, then one ...
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203 views

p-value adjustment for Local Moran's I statistic (LISA)

I'm working with some exploratory spatial analysis in R using spdep package. I came across an option to adjust p-values of local indicators of spatial association (LISA) calculated using ...
6
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1answer
872 views

How to apply multiple testing correction for gene list overlap using R

I have 2 studies looking at the patient response to the same drug. Study 1 found 10,000 genes expressed above the background and 500 of them are differentially expressed and referred to as the drug ...
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1answer
129 views

How can I perform a familywise error rate correction for Johansen cointegration tests?

I want to test multiple possible cointegration relationships with the Johansen cointegration test. I'm currently using the urca package in R with the ca.jo test. I was going to use the Bonferroni ...
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2answers
12k views

Bonferroni adjustment in SPSS - what does it do?

first post, so go easy... I'm probably being a bit simplistic here, but from what I understand the Bonferroni post hoc test is simply when we adjust the alpha to account for inflated error when ...
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1answer
105 views

Question regarding Bonferroni correction

Prove the following version of the Bonferroni inequality- $$P\left(\bigcap_{i=1}^kA_i\right)\ge1-\sum_{i=1}^kP(A_i^c)$$ When creating simultaneous confidence interval, what are $A_i$ and $A_i^c$? ...