In hypothesis testing, the $p$-value refers to the probability of seeing a result as extreme (or more so) than the one observed, given that the null hypothesis is true. When the $p$-value is small, then there is good evidence that the null hypothesis is false, since it would make the observed data ...

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Permutation test and p-value

I construct a permutation test in order to see If two samples come from the same distribution or not. I have two vectors $x,y$ that hold values of sampled values from two populations and the test ...
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28 views

Excel: Computing a pvalue [on hold]

An event has an expected probability of .4. After 100 trials, the event occurred 30 times. How can the pvalue be computed in Excel?
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35 views

sample size too large? [duplicate]

I always thought larger sample sizes were better. Then I read something somewhere about how when sample sizes are larger, it's easier to find significant p-values when they're not really there (i.e., ...
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298 views

p-value subtlety: greater-equal vs. greater

As I am reading Wassermann's book All of Statistics, I notice a fine subtlety in the definition of p-values, which I cannot make sense of. Informally, the Wassermann defines the p-value as [..] ...
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58 views

Distribution of p-values in this thought experiment?

I'm trying to check whether my clustering was informative above and beyond random clustering. This is my thought experiment to do it, can someone help? Suppose I have a large number, $N$, groups. ...
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30 views

Bootstrap glm and extract pvalue

I am running a glm model using bootstrap, I can extract the coefficient mean and the confidence intervals for all the factors in my model. But how can I get the pvalue from there? Model: ...
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9 views

Compute effect size based on simulation using different lists of different length

For my research purpose I wrote a small simulation to compute an empirial p-value based on an input gene list and a reference gene list. The idea is to check for each gene in the input gene list, the ...
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20 views

Tukey HSD, insignificant p-value when the confidence interval does not contain 0?

I am using TukeyHSD to do multiple comparisons. I am seeing strange results for some of the pairs: the adjusted p-value is greater than the specified significance level but the corresponding ...
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31 views

How do I interpret the p value returned in scipy's Mann Whitney U test?

I have a program in which I need to perform an action based on what results of a Mann Whitney U test are. I know the criteria that need to be met, but I would still like to understand what the results ...
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36 views

Implementation of Bayes posterior predictive check

I have a question concerning the implementation of a bayes posterior predictive check. Let us assume i have this model (implementation is in R and jags): ...
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15 views

how to report p-values from t-test and ks test in the same table for publication?

I want to show in a table that two samples are different in a number of attributes (or not different). I want to report the mean, st.err. and the stars at conventional values of p-value from a t-test ...
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46 views

Is reverse of p-value also uniformly distributed?

If p-value, $p(F|H_0)$, is uniformly distributed $U[0,1]$, so is true to say, that $p(F|H_1)$ is also uniformly distributed $U[0,1]$ or even more: is it true $p(F|H_0) = 1-p(F|H_1)$? I'm not sure if ...
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independent replicate experiments yielding contrasting results

This is a though, simple experiment, for thinking efficiently about a real problem much more complicated... Imagine a simple experiment, trying to answer a simple question. For example, is body ...
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45 views

Why do we compare p-value to significance level in hypothesis testing of mean?

I know that: p-value = P(observed or more extreme outcome of sample mean | Null hypothesis is true) But why do we compare it with significance level (alpha) while determining if it is high or low? ...
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33 views

Analysis of the Benjamini-Hochberg adjusted p-values

I have: Condition #1 : 5 independent objects (1 object = a time series) Condition #2 : 5 independent objects My GOAL: test H0 that using condition #1 gives different results from using condition ...
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26 views

p-values, prior probabilities

I've got a set of N normal independent normal distributions, each representing a signal. I also got a new data sample, a vector $v$ of size Nx1. Now let's say I compute the p-value using the ...
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60 views

How to calculate p value from distribution of test statistic

I was wondering how I can calculate p-value from a distribution of test statistic manually? Regards,
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31 views

p-value over q-value?

I am trying to figure out when (during multiple testing) to use $p$-values and when to use $q$-values. This student thesis explains how this particular theorem (Eq. 11 in the paper) allows one to ...
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Weighting p-values

In KEGG pathways (Kyoto Encyclopedia of Genes and Genomes) data set designed as columns and rows. The columns consisted of 50 pathways and the rows are 189 genes. The genes can work in certain ...
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72 views

Interpreting results of chi-squared

Situation: A/B test of a single website change on a landing page. Alternating visitors to the landing page are shown a variation. The goal is to convert more visitors into customers. With data that ...
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23 views

P value distribution skew & hypothesis testing

On this page it says ...if HA holds, the p-values have a distribution for which values near 0 are more likely than values near 1. However the p-values may have a distribution that is not ...
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77 views

GLMER: Conflicting results from p values and bootstrapped confidence intervals

Please don’t be shocked by the amount of code in this post, this problem is (hopefully) not as complex as it seems. This dataset ...
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77 views

R lme4 1.1-7 glmer: p values for fixed effects in summary() and likelihood ratio test comparison

I'm using glmer() with a binomial response variable. My optimal model has two fixed effects (flow and DNA) which in summary() show a non-significant p value but ...
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p-value test for comparing classifiers

I have to use p-value test to compare two classifiers. I am getting the error vectors of 2 hypothesis and I am using their difference as an input in ttest function of MATLAB ...
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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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36 views

Equivalence of p-values from Jonckheere-Terpstra test and Kendall's tau

I'm using the Jonckheere-Terpstra test to confirm whether an interval variable, distributed across five levels of an ordinal variable, display a significant trend. I'm using the clinfun package, ...
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38 views

Big difference in p-value from permutation test

I have roughly 60 values of discrete temperature satisfaction votes ranging from 0 to 4. In the figure below I have grouped the votes depending on the daily number of hours the individual occupants ...
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Meta-analysis - generating null distributions of test statistics.

I'm having trouble obtaining p values for effect sizes from a meta-analysis because the distribution of t-statistics is not normal. The analysis involves eight studies, each containing measurements ...
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35 views

logistic regression with GLMM (and p-values)

It seems that I'm a little bit confused with the different ways to achieve its goals in the statistics’ world (and the R’s universe), so I’m asking your help about issues with which I'm struggling. ...
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47 views

Testing uniformity of data

I need to test if a vector of observed values are uniform distribution. Lets assume: This values are not a sample, but my entire universe. I have a dataset of 12000 observations, where most of the ...
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31 views

What does a large P value mean with regards to patients lost during follow-up?

What does "P=0.45" mean in this case? Complete 1-year follow-up data were obtained for 98.1% of the patients (11 were lost to follow-up in the angiography group and 8 were lost to follow- up ...
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31 views

Wilcoxon Rank Test or T-Test? [duplicate]

What data analysis is better? or fit for my data? I've used Likert scale for my questionnaire (1-5) and I have 387 respondents. Wilcoxon Rank Test or T-Test?
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1answer
44 views

Changing polynomial degree leads to changing p-values in OLS regression

I have a question about interpreting coefficient $p$-values when fitting a polynomial function with ordinary least squares. When I sequentially fit a linear, then quadratic, then cubic etc. ...
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201 views

Using brute force to get exact p-value instead of Chi-Squared Test of Independence

Background I have the following contingency table ...
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82 views

Effect size for a one-sample t-test

Imagine I work in a screw factory (which is not true). We have been producing a series of 5cm-long (on average) screws for years. I want to modify the production parameters in order to save some money ...
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78 views

Statistical significance test: One way Anova and Kruskal-Wallis test

I was comparing data between two groups and for each group there was six samples. My data are as follows: group 1: 103.56, 103.32, 103.32, 104.27, 103.56, 103.8 group 2: 97.16, 97.16, 96.69, 98.58, ...
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121 views

How are the p-values in the glmer (lme4) output calculated?

The output of models built using the glmer function in the package lme4 automatically includes p-values. What method does lme4 use to calculate these p-values? I can't seem to find this information ...
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64 views

P values depend on researchers' sampling intentions

John Kruschke has written widely on the misleading information provided by p values. I understand nearly everything he says, although there is one aspect I am a little confused about. Kruschke ...
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p values for percentage results with sampling bias

I have calculated a phylogenetic tree for different viruses which I can group in ten clades (groups). The samples i used to generate the tree, originate from five different countries and fife ...
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44 views

Glm with Poisson in R with no p-value?

I've been doing glm and thought I had it cracked but looking at some sites for interpreting results I realised R had displayed my results oddly. ...
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12 views

What is a “(in)dependent p-value”?

Does someone know what "independent p-values" or "p-values independently distributed" means? And the "dependence structure among test statistics"? Thanks in advance
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40 views

P-values distribution meaning

Could anyone tell me what changes in the p-value distribution mean? I mean, for example, what does mean that the p-values follow a uniform distribution? and what happens if the p-values distribution ...
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23 views

How to study the property of a score e.g. its variance in R

I'm trying to develop a score for biomarker discovery in two-class high throughput biological data. At this stage the significance of the score (p-value) is estimated by permutation of the class ...
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62 views

Permutation for large sample sizes (and z-test)

I was trying to do a permutation test on a large amount of temperature observations in R. Approximately 1700 temperature observations (g1) from one place and 2 ...
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64 views

How to calculate p value from ANOVA function for LMM results?

I have used ANOVA function so that I can get the overall p value of significant factors: ...
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62 views

A doubt on the definition of p-value

The p-value is the probability, under the assumption of the null hypothesis $H_0$, of obtaining a result equal to or more extreme than what was observed at given data. This means, if I were to ...
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43 views

How to interpret underrepresented low p-values in Multiple Testing?

This is, I hope, quite a simple question. Being new to the concepts and methods of Multiple Testing, I've been histogramming some of the p-values I've been computing in my genomics research. What I ...
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49 views

P-value multiplied by 2 for two tail hypotheses F-test

There is a following answer to an exercise in a text book: The hypotheses are \begin{align*} H_0 &: Var_1 = Var_2\\ H_1 &: Var_1 \neq Var_2 \end{align*} Computation: $f = 78.800/913.333 = ...
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82 views

Calculate odds ratio and confidence interval from p-value

I am working with summary statistics from a genome-wide association study (p-values, odds ratio, standard error). The test statistic in the dataset was inflated, so I have had to correct for this ...
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Is the “hybrid” between Fisher and Neyman-Pearson approaches to statistical testing really an “incoherent mishmash”?

There exists a certain school of thought according to which the most widespread approach to statistical testing is a "hybrid" between two approaches: that of Fisher and that of Neyman-Pearson; these ...