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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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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52 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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8 views

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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26 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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37 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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20 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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45 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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39 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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55 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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1answer
34 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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25 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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47 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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763 views

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 ...
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2answers
51 views

Confidence intervals which contain 1 but the z test and p value are significant

I calculated the confidence intervals for the regression coefficients using the formula: SE X 1.96. I then took this value away from the regression coefficient to get the lower confidence level and ...
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1answer
38 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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17 views

How To Determine Association Plot in R and p-value

I have created a contingency table and an association plot in R and I am not quite sure how to interpret it. Here is my contingency table: ...
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18 views

FE, RE and p-values

Am not so good with econometrics but I have to estimate two equations with Fe and Re. I have 8 vars which translate to 6,006 obs. the problem is that all the p-values are higher than 5%, does this ...
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21 views

Interpret transformations in Granger causality analysis

I have two time-series with positive counts which roughly look like http://www.google.com/trends/explore#q=italy . I'm new to time series analysis, so I used ...
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5answers
221 views

Does $r$-squared have a $p$-value?

I seem to have confused myself trying to understand if a $r$-squared value also has a $p$-value. As I understand it, in linear correlation with a set of data points $r$ can have a value ranging from ...
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36 views

standard score or p value

I have two groups of data, each contains five sets. Each of them has a standard score. I would like to compare them. However I don't know if it is good to directly compare standard scores. As you ...
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1answer
34 views

Wilcoxon tests in Doronix Math Toolbox

I'm using Doronix Math Toolbox. They have statistical functions (http://www.doronix.com/statistics.html). I can't figure out how they are finding p-value in ranksum and signsum tests. Does anyone know ...
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15 views

Determining Sample Size to Show Increase in Disease Prevalence

A prof and I are trying to figure out how many samples a study would need to show a certain % increase in disease prevalence, but I'm not sure I'm doing this correctly. Basically we want to know how ...
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17 views

Correct for multiple testing using Spearman

I am using a Spearman correlation for my dataset. I have three conditions and I want to know whether there is a correlation per condition. To do this I filter e.g. condition 1 and correlate variable X ...
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81 views

Too many p-value less than 0.0001 is alarming?

Can anyone explain why having too many p-value less than 0.001 is alarming? Like what happens to my model right now: All independent variables are categorical except for Calendar_Year. There are ...
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48 views

Name for the Bayesian posterior probability that a regression coefficient is larger than zero

I have the following logistic regression: $$ \text{logit} (y) = \beta_0 + \beta_1\, x $$ from which I can estimate the following posterior probability (using a Bayesian approach): $$ ...
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29 views

Logistic Regression - Binning - Interpretting p values

My name is Abhi and I am trying to teach myself regression by solving some practice problems available on the internet. I am using RStudio as my development environment. Problem Statement Given the ...
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44 views

An exact paired perm.test is returning a p-value of 0 for large sample sizes

I'm trying to find the p-value from an exact paired permutation test. For small samples it works fine: ...
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1answer
41 views

Is positive coefficient of price correct in a multiple regression model

I am currently undertaking forecasting of energy sales (kWh) for our industrial customers. From historical data gathered from 1993 to 2013, a graph of price per kwh against sales kwh shows a positive ...
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28 views

Best proportions test based on counts (accuracy, distribution, etc)

I'm trying to compare two sets of counts over totals. For example, subject 1A will have 40 out of 600, and subject 1B will have 3 out of 20. How do I compare these proportions and counts while taking ...
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39 views

Iterative Addition of Variables to Model Based on P Value

Suppose I have 64 columns that I have chosen out of 500+ columns based on the fact that they have the highest pairwise correlation (is this a good way?). I take 16 of these columns and run a simple ...
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18 views

Am I using Fisher method correctly?

Suppose I want to test the hypothesis that speed of light is always below $c$ (note: regardless of the medium). [Also, this is just a fake example, so pretend we don't know any physics theory] Now, I ...
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2answers
101 views

P-values equal to 0 in permutation test

I have two datasets and I would like to know if they are significantly different or not (this comes from "Two groups are significantly different? Test to use"). I decided to use a permutation test, ...
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2answers
33 views

Overall Significance vs. Individual Variable Significance in Mutliple Regression

I'm running a statistical analysis for work in which I'm trying to determine which (if any) key economic indicators influence our sales. Here is the summary data that I'm getting when I run a ...
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44 views

What are the null and alternate hypotheses? Will you use a left, right, or two-tailed test?

Ben has a coin which he claims is weighted in a way so that when he flips it, heads appears more often than 50% of the time. He tries to prove it to you by flipping the coin 100 times, which ...
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33 views

Significance of varibles after stepwise regression

I did stepwise regression with my multiple regression model and using AIC as a measure of fit with the step function in R. Afterwards some variables that the ...
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78 views

SPSS: Pearson's r not significant but confidence intervals do not include 0

I have calculated the value of Pearson's r between two variables in SPSS, two tailed. Sample size is 81. The r value is -.21. The p value is .06. When I compute the 95% confidence intervals using ...
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293 views

Interpreting one- and two-tailed tests

How do you report results that give you a p-value of 0.08 for a two-tailed test and a p-value of 0.04 for a one-tailed test? Generalizing the issue, if you obtain a p-value between 0.05 and 0.9999 ...
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79 views

F-statistic value is too high for my model

Number of obs = 501 , Method: Fixed-effects regression Number of groups = 101 F( 10, 100) = 3422.31 , Prob > F = 0.0000 , ...
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44 views

Quantifying Potential for Violence/Espionage

I am planning a seven-question Likert-type survey with a "1 to 10" scale. The questions I am asking in the survey are to assess an individual's risk factors (how much risk they present to an ...
3
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50 views

two-sample Kolmogorov-Smirnov test in R p-value confusion

I'm confused about the appropriate interpretation of p-values returned by the two-sample Kolmogorov-Smirnov test (ks.test) in R. In slide 23 of this presentation about non-parametric two-sample ...
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82 views

Understanding $\chi^{2}$ and Cramér's $V$ results

I have two groups of buyers, A and B, and I want to test whether the difference between the percentage of them who would buy a ...
3
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2answers
202 views

Is p-value also the false discovery rate?

In http://surveyanalysis.org/wiki/Multiple_Comparisons_(Post_Hoc_Testing) It states "For example, if we have a p-value of 0.05 and we conclude it is significant the probability of a false discovery ...
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1answer
152 views

interpretation of little's mcar test

My little's MCAR test revealed chi-square = 27.120, DF = 1974, and sig. = 1.000. 74 items and 151 cases. So, can I concluded that the data were missing completely at random since the p-value is not ...
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144 views

How to explain borderline p-values to non-stats people

I ran an OLS regression, and the p-value of one variable is 0.065, which is more than the threshold to consider statistically significant. However, it's not too bad either, as my data has only 300+ ...
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2answers
26 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 ...
3
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1answer
192 views

Calculate a 95% confidence interval and p-value for the change in C-statistic using bootstrap with R

I am using boot() and boot.ci() to furnish confidence intervals for the difference in the $c$-statistic (AUC) between models ...
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4answers
318 views

What is the meaning of a large p-value?

I understand that the $p$-value is the conditional probability of observing the test statistic or something more extreme given that the null hypothesis is true. I have read the great explanation by ...
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40 views

Interpretation and understanding results from a chi square test for independence

I'm making a chi square test on data that has information about students. I want to find out whether there is a relationship between how well the students did on a particular test and the level of ...