Tagged Questions

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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26 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 ...
2
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0answers
16 views

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 ...
3
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1answer
60 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 ...
0
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0answers
13 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 ...
1
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0answers
67 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 ...
0
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1answer
41 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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0answers
18 views

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 ...
3
votes
1answer
23 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 ...
2
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0answers
18 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, ...
2
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1answer
36 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 ...
0
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0answers
10 views

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 ...
2
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0answers
25 views

How do I calculate p values of a linear regression given the covariance matrix and fit coefficients [migrated]

I have performed a linear regression in C using the GSL library. I've performed the same regression in R. I can access the p values for this regression in R using the "summary" command. In C, I have ...
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0answers
16 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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0answers
43 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 ...
1
vote
1answer
30 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 ...
0
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1answer
25 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?
3
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1answer
39 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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0answers
21 views
4
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1answer
196 views

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

Background I have the following contingency table ...
4
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2answers
64 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 ...
2
votes
1answer
51 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, ...
3
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1answer
81 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 ...
3
votes
1answer
60 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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0answers
13 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 ...
1
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0answers
37 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. ...
1
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0answers
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
0
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1answer
39 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 ...
0
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0answers
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 ...
3
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0answers
51 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 ...
0
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0answers
55 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: ...
0
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0answers
58 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 ...
3
votes
1answer
38 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 ...
0
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0answers
35 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 = ...
0
votes
1answer
62 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 ...
23
votes
4answers
800 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 ...
2
votes
2answers
60 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 ...
4
votes
1answer
41 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 ...
0
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0answers
23 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: ...
0
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0answers
19 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 ...
0
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0answers
23 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 ...
12
votes
5answers
236 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 ...
0
votes
0answers
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 ...
0
votes
1answer
40 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 ...
0
votes
0answers
18 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 ...
0
votes
0answers
20 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 ...
0
votes
1answer
97 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 ...
2
votes
0answers
51 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): $$ ...
0
votes
1answer
34 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 ...
1
vote
2answers
52 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: ...
2
votes
1answer
59 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 ...