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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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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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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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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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
29 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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263 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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37 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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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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55 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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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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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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64 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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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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Questions about Factorial MANOVA

I have a few questions about the factorial MANOVA below which I hope can be answered: 1)What type of follow-up tests should be done after finding significant interaction effects in a factorial ...
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312 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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153 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 ...
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522 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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55 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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6k 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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Families for Bonferroni correction

Suppose I have 6 groups of mean: A, B, C, D, E and F. I compare A, B and C as a family with a Bonferroni test, then D, E and F as a separate family and a separate test. Now what if I then also want ...
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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 $A_i^c$? ...
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1k views

Two questions about Bonferroni adjustment

I have two questions about Bonferroni adjustments: 1). Can one use the Bonferroni method to compare independent groups? The reason why I ask this is it seems that many examples I've encountered ...
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1answer
229 views

Determining number of tests to correct for using Bonferroni

I am doing final revisions to my dissertation, which includes a large number of regressions. I have six outcome variables (DVs) and I am testing the effect of four primary (correlated) IVs, but I am ...
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Is this a valid method to control the FWER?

I have a huge number, say $M$, of hypotheses that are potentially correlated. I have a dataset $D$ of random samples from an unknown distribution and I want to do test the hypotheses for significance ...
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1k views

Anova repeated measures is significant, but all the multiple comparisons with Bonferroni correction are not?

I counducted a mixed model ANOVA with time as the within subjects variable (3 levels) and group as the between subjects variable (2 levels). All is significant (time, group, and timeXgroup). To test ...
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Post hoc test in a 2x3 mixed design ANOVA using SPSS?

I have two groups of 10 participants who were assessed three times during an experiment. To test for differences between groups and across the three assessments, I ran a 2x3 mixed design ANOVA with ...
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542 views

Non parameteric tests for 2*2 mixed design

I have 2*2 mixed design, where the two factors are time and group. The time levels are pre- and post-intervention, and the group levels are control and intervention. If I were using a parameteric ...
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242 views

Strict Bonferroni - looking for p value

I run 18 exploratory regressions and would like to know what the strict Bonferroni p-value would be. Nine regressions are negative binomial regressions with 4 predictor variables, the other 9 are WLS ...
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Bonferroni post hoc test does not reveal significant differences between groups [duplicate]

Possible Duplicate: How can I get a significant overall ANOVA but no significant pairwise differences with Tukey's procedure? I used a repeated measures ANOVA for my dissertation, with ...
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1answer
122 views

Best way to go about correcting for multiple comparisons (or should one even) for a small dataset?

Disclaimer: I have a very minimal stats background and am just getting into this stuff. Corrections to any terminology I use or an improved rephrasing would be super appreciated. I have a simple ...
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335 views

Bonferroni correction in generalised linear model

I am running a generalised linear model in R. I have a single response variable and a maximum of 4 possible explanatory variables. I am adding each explanatory variable to the model sequentially, ...
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1answer
821 views

Permutation tests in R for correlations

What's the easiest way to run permutation tests for a bivariate Pearson correlation matrix in R? I have tried running MPT.Corr, Multivariate Permutation Test for Correlations by Urbano Blackford et ...
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2k views

Bonferroni and Greenhouse-Geisser corrections with repeated-measures ANOVA

I guess my question comes in two parts: Following a 1x7 repeated-measures ANOVA, I carried out 3 pre-planned tests. Two were t-tests between 2 of the conditions. The third is a 1x6 ANOVA (to test ...
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435 views

Multiple comparisons process using Kruskal-Wallis, G-Test and corrections

I want to know if changing a button color has a positive effect on different measures (see the 4 measures below), using the following process: There's a default button, which is the fixed control ...
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Sidak or Bonferroni?

I am using a generalized linear model in SPSS to look at the differences in average number of caterpillars (non-normal, using Tweedie distribution) on 16 different species of plants. I want to run ...
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723 views

Fisher's exact test and large tables with pairwise

I found that it is possible to look at adjusted residuals and treat them as a z-score and then use a two-tailed test to find a p-value. The problem is how do you calculate adjusted residuals on what I ...
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417 views

Sample-size calculations for Benjamini-Hochberg, Westfall-Young, Holm-Bonferroni methods

I'm currently setting up an experiment where we might want to do multiple comparisons (i.e. comparing several treatments with a control at the same time). It is pretty straightforward to calculate the ...
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161 views

What is the basis for adjusting critical values in multiple t-tests?

Let's say I have three samples: control, A, and B. (I am assuming basic things about sampling like no bias, no confounding factors, and independence in selecting samples.) I want to see if there is a ...
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475 views

What type of error correction do I have to use after Wilcoxon matched pairs test?

Do I have to use Bonferroni's or Holm's corrections? Please see this previous question for my example data and the design. (Shortly, I have three or more dependent groups.)
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Repeated measures ANOVA in R and Bonferroni adjusted intervals

If somebody can tell me what R commands I need to use for a repeated measures ANOVA, I'd really appreciate it. I have trouble with the random term. I've seen ...
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Maximum number of independent variables that can be entered into a multiple regression equation

What is the limit to the number of independent variables one may enter in a multiple regression equation? I have 10 predictors that I would like to examine in terms of their relative contribution to ...