Questions tagged [bonferroni]

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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MANOVA and Hotellings tests

I have a matrix with 33 columns, the matrix can be found here: https://pastebin.com/3pAAGNti Each line of the matrix belongs to a specific group, from 1 to 8. The group number is stored in the last ...
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Running tests over many samples. How to deal with many p-values?

I have 2 sets of 40 000 independent datasets (composed of 10 000 elements each), that I am comparing using an Anderson-Darling test. More precisely, I compare corresponding subsets of my two sets, so ...
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Trouble Understanding Holm-Bonferroni Correction

I have a bit of trouble understanding the Holm-Bonferroni correction. For the normal Bonferroni correction you simply divide your alpha level by the number of tests. For example, if I have 3 tests, I ...
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Calculating alpha level for Bonferroni

I have 4 null hypotheses. I want to conduct 4 two-way mixed ANOVAs (one between-subjects factor and one within-subjects factor) for each of my 4 dependent variables. I will use the same between-...
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How does the Bonferroni correction benefit from independent tests?

In section 2 of this PDF, it is stated that the Bonferroni correction "benefits" from the tests being independent, and that if tests are not independent, the Bonferroni correction could be ...
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Not understanding adjusted p values with Holm's method. Highest value in series divided by 1

I'm finding an issue while adjusting p-values with Holm's method I cannot understand. It's not a problem in my actual data, but I would appreciate any help to understand the issue. To show the ...
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Correction for multiple testing in Multiple regression analysis

Correction for multiple testing (e.g. Bonferroni correction) is recommended when multiple statistical tests are performed on same data. In multiple regression analysis, multiple testing is integral ...
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How to get the standardized z-statistic from dunn.test-package in R?

Sorry if this is a trivial question, but I couldn't find anything on it. I am running a Dunn-test with the dunn.test-package: ...
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Is a multiple testing correction warranted when you test for specific outcomes?

Suppose we are interested in the association between a binary exposure (0 or 1) and a binary outcome in two subgroups of two cohorts. That is, we have subgroups A-, A+, B- and B+ with $n_{A-} + n_{A+} ...
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Box's M Significant and One variable in Leven's test failed for quality of variance SPSS

I am doing a MANOVA test as part of a psycology project and have to use MANOVA Box's M gives a sign value of less than 0.05 (stated to be used on imb's website) but greater than 0.001 (stated to be ...
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Comparing different samples from different years: ANOVA?

I have been collecting data for 10 consecutive years. Once in each year different participants (N=110/Year) had to rate the importance of each one of 30 different social values, on a Likert scale (1-5)...
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Multiple testing between treatment groups, and between subgroups within treatments. Bonferroni correction required?

I have a data set that is structured such that I have four treatment groups with 6 samples each; 3 samples in each treatment were taken at an early time point, and the other three were taken at a ...
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Is there any consensus on adjusting p-values for multiple tests?

I'm confused as to when adjustments for multiple tests need to be used. I'm an undergrad who's familiarising himself with stats, so apologies if my question sounds dumb, but I haven't found any ...
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Why is the Tukey method not appropriate for covariance analysis when estimating treatment effects?

In the book 'Applied Linear Statistical Models' chapter 22 it states that the Tukey method is not appropriate for covariance analysis. The context is in estimation of treatment effects. Instead, when ...
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Bonferroni correction applied to models of multiple linear regression

I am doing an article in which we assessed the association between the six domains of a scale and clusters of activations. I conducted linear regression analyses between the clusters of activation (5) ...
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Multiple hypothesis and multiple comparison with GLMMs

I have a data set with 20+ variables from the same underlying subjects (animal nests) under three treatments. I have modeled the effect of treatments on each of these variables using seperate GLMMs, ...
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Do I need to use Bonferroni correction?

I have a dataset containing the selling price of mineral stones that were sold in five different countries (namely Germany, France, Italy, Belgium and Spain). I am running multiple t-tests check if ...
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Should multiple adjustedment correction be applied here?

I have a question. I'm analysing an article for an assignement. In this study there are two groups (normal d-dimer vs elevated d-dimer). The study compaires the mean of the groups for multiple ...
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Please can somebody clarify p adjusted values ( via Bonferroni correction method)?

I am using metabolite data generated from LC-MS. I am making comparisons between two groups at a time, and need to account for Type 1 error and multiple comparisons, so I have utilized Bonferroni ...
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How to adjust p-value with Bonferroni correction?

I think this is a simple question, but for which I've found conflicting answers around. Let's say, I measured a biomarker in a group of patients with 5 different methods and I want to perform ...
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Bonferroni Adjustment to Multipe Comparisons AND Multiple ANOVA's

I'm running four one-way ANOVAs using a different DV each time. Each ANOVA has one DV and four IV condition levels. I currently have each ANOVA set up in a different data file. I would have liked to ...
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Multiple metrics on two groups, Bonferroni correction?

I have 8 sets of data before and after a given treatment. Let's call them: a, b, c, d (before), and a', b', c', d' (after treatment). These sets are paired, in the sense that "a" and "a' " represent ...
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Do I have to correct for multiplicity twice if I re-run a comparison with one more hypothesis during incremental testing?

Let's say I have a set of hypotheses ordered in time. These are about comparison to some baseline moment: $H_{t1 vs. baseline}$, $H_{t2 vs. baseline}$, $H_{t3 vs. baseline}$, ... I have 10 time ...
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Incremental hypotheses testing - finding the first occurrence of three consecutive significant effects

I cooperate with a scientist, who measures some effect of a certain procedure over time: t0, t1, t2... Then, the scientist filters out all trivial effects, to avoid reporting statistical significance ...
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Correction p-value with the Bonferroni correction

I have done an analysis using SPSS. I would like to compare the situation before and after treatment in the same patient, so I used the Wilcoxon test (not normally distributed). Now I look at 3 ...
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Bonferroni correction in one-way ANOVA for one dependent variable

I have a quick question I hope somebody could help me with; If I have two one-way ANOVA's in my research just comparing the means of three age groups for a single dependent variable (so two seperate ...
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Statistical testing after adjusted p-values(holm correction)

I have 5 different samples(P1,P2,P3,P4 and P5) with 4 replicates(a,b,c,d).I did paired t-tests with the null hypothesis that there is no significant difference when compared to the control group at p=...
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Do we need the Bonferroni correction when creating confidence intervals from a dynamic linear model?

This is how we would recover the AR1 parameter and the variance of the residuals in an AR1 model using a state space model. ( I saw this code here ) ...
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Family Wise Error After Applying Benjamini-Hochberg Correction to Control False Discovery Rate

I did a multiple comparison simulation. Each round contains 100 tests and each test has 2 groups. 80 of them have the same group mean(true H0). 20 of them have different group means(true H1). Alpha is ...
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How to derive Bonferroni's Inequality using Boole's Inequality?

I'm trying to derive Bonferroni's inequality using : $$P(\cup^{\infty}_{i=1} A_i) \leq \Sigma^{\infty}_{i=1} P(A_i)$$ for any sets A_1, A_2, ... (Boole's Inequality) The result I want is (Bonferroni'...
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PERMANOVA planned comparisons

My question is two-fold. I am planning to run pairwise comparisons of several variables after a 2-way fixed factor PERMANOVA. Is it expected to do some kind of correction method like Bonferroni when ...
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Defining the number of multiple comparisons for a Bonferroni correction

I have a 4 (Time) x 3 (Size) x 3 (Type) Repeated Measures ANOVA. Since SPSS does not allow post-hoc analysis for repeated measures, I had to run individual t-tests one by one. Assuming that I am only ...
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MANOVA contrast results p-value in SPSS - Bonferroni correction required?

I am running a MANOVA with 2 IVs(2*3) and 4 DVs. I want to test the effect of the 3-level IV using a Helmert contrast: to compare if level 1 significantly differs from the mean of levels 2 and 3, as ...
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What counts as a comparison?

Say we have a test in which we are comparing many variables to a dependent variable, using different methods. Say ttest, chi2 and then finally a multiple regression on parts of the data. Would we ...
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How to conduct Holm's procedure for two-sided Wilcoxon signed rank test when conducting pairwise comparisons for multiple classifiers?

I am trying to compare the accuracies of m classifiers on multiple datasets. Following the suggestion of the JMLR'16 paper "Should We Really Use Post-Hoc Tests Based on Mean-Ranks?", I have decided to ...
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conducting a multilevel model with a continuous variable and categorical variable in r (+ post hoc)

I conducted a study in which I presented three types/blocks of visual stimuli (neutral stimuli in baseline, negative stimuli, neutral stimuli following negative stimuli). To examine the relationship ...
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A one-way ANOVA for multiple comparison

Cheng, H., & Liu, S. (2019). Haptic Force Guided Sound Synthesis in Multisensory Virtual Reality (VR) Simulation for Rigid-Fluid Interaction. In 2019 IEEE Conference on Virtual Reality and 3D User ...
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Multiple comparison adjustment with multiple outcomes, measured over time

I am trying to work out the most appropriate way to adjust for multiple comparisons. I have 20 biomarkers which have been measured at 4 timepoints (baseline & three unevenly spaced follow-ups). I ...
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Does “uniformly more powerful” also mean the same or fewer type I errors?

Does a "uniformly most powerful" (UMP) test also imply that it will make the same or fewer type I errors? Specifically, is there ever a (statistical, not convenience) reason to use a simple Bonferroni ...
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Significant main effect but no interaction which post hoc test to do?

I have an experiment looking at the effect of rearing condition on development of the number of neural networks (ensembles) in mice. I therefore have two factors (Age 3, 5, 7 dpf) and Rearing ...
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Multiple testing on the same dataset

I have a dataset with n = 76 independent test subjects (rows) and 3 dependent variables (columns) (which are related as a process taking place over time). For the example below I will assume I have ...
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Alternative for Bonferroni correction for two groups using SPSS

I have two (2) groups of children that have been tested on the same series of tests. Trying to check a series of hypotheses, I compare the performance of both groups on these tests, using one-way ...
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I have performed three likelihood ratio tests on a factor in R. Do i need to adjust the p values?

I am a student doing a thesis for zoology. I am looking at how factors like season (winter/summer), fencing (inside fence/outside fence), and the interaction between season and fencing affects ...
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When do we “stop” using multiple correction techniques?

I understand when performing a simple t-test, we typically control the type -1 error rate at $\alpha = .05$. This signifies that if the null hypothesis holds, the data will "incorrectly" reject the ...
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Same value P-Values - Holm-Bonferroni

When using a Holm-Bonferroni adjustment method or the like, how to you treat multiple p-values of the same value when ranking? For instance, I have the unadjusted p-values: ...
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Do I need a Bonferroni correction on a 2x2 chi-squared analysis?

I'm really hoping someone here can help. I have performed a chi-square test of independence, looking at men/women and early/late drop out from therapy. I have a p-value of 0.047. Do I need to do any ...
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How to adjust P-Value for Multiple Tests

I'm not sure if this is answered or not because there's a lot of these questions and the ones I looked at didn't answer this. If I were to say, have five independent variables of interest and one ...
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Considering pre-tests in family-wise error correction doing an ANOVA

When I do multiple tests on a dataset, I need to correct for the family-wise error (e.g. using Bonferroni method when performing multiple pairwise t-tests). If I do an ANOVA, I need to make sure that ...
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Apply Fisher's exact test on multiple class

I am testing the presence of viruses within samples, which are matched 'normal', 'cancer' and 'metastasis'. I am testing the presence of viruses at species, family and order level. For instance, I ...

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