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23 votes
Accepted

What does the assumption of the Fisher test that "The row and column totals should be fixed" mean?

In my opinion, the source that you link to is wrong in that it is confusing conditioning with assumptions. Fisher's exact test conditions on the margin totals, meaning that it does not use any ...
Gordon Smyth's user avatar
  • 13.1k
19 votes

Infinite upper confidence interval using Fisher exact test in R

There's a one-sided confidence interval because you asked for a one-sided test
Thomas Lumley's user avatar
16 votes

When and how to avoid inappropriate use of Fisher's exact test

It's hard to read this quotation & not surmise that the author considers it a mere blunder to use Fisher's Exact Test when the marginal totals of a contingency table are not fixed by design. "...
Scortchi - Reinstate Monica's user avatar
15 votes

Why do odds ratios from formula and R's fisher.test differ? Which one should one choose?

From the help page for fisher.test(): Note that the conditional Maximum Likelihood Estimate (MLE) rather than the unconditional MLE (the sample odds ratio) is ...
13 votes

Analysis of Danish mask study data by Nassim Nicholas Taleb (binomial GLM with complete separation)

Your 2-sided test implicitly allots exactly half of your 5% significance level to "masks are harmful" ($M_-$) and the other half to "masks are beneficial" ($M_+$). To a Bayesian ...
fblundun's user avatar
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12 votes

How can we have multiple "exact" tests?

What make and exact test exact is that it uses the actual distributions of the null hypothesis (e.g. binomial or hypergeometric or multinomial distributions) rather than approximations (e.g. normal or ...
Henry's user avatar
  • 40.4k
11 votes

Fisher's exact test vs. differential gene expression

As has been thoroughly discussed on this site, Fisher’s “exact” test is not very accurate, the ordinary Pearson $\chi^2$ is more accurate, and you can save a lot of computing time by using it. A more ...
Frank Harrell's user avatar
10 votes
Accepted

Interpretation of the Fisher-exact test

The fisher's exact test in R by default tests whether the odds ratio associated with the first cell being 1 or not. That said, you can interpret the odds ratio 0.53 as: the odds of being male for a ...
SixSigma's user avatar
  • 2,322
10 votes
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Fisher exact test on 4 x 3 table, with low count?

Having observed zeros is not an issue for a Fisher Exact test -- nor indeed is it a problem for a chi-squared test (it's not clear why you think this would be a difficulty with an exact test; if you ...
Glen_b's user avatar
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10 votes
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Interpreting zero odds ratio from Fisher's exact test

If in a 2-by-2 table, we let $n_{11}$ be the counts in (1,1) cell, $n_{12}$ the counts in the (1,2) cell, $n_{21}$ those of cell (2,1) cell and $n_{22}$ those of cell (2,2), then the sample odds ratio ...
utobi's user avatar
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9 votes
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Fisher's Exact test implementation in R

You have chosen to do a one-sided test and, obviously, order is important in a one-sided test. Your first call to fisher.test is testing the null hypothesis Pct1 = ...
Gordon Smyth's user avatar
  • 13.1k
9 votes

Sample size calculation in COVID-19 study

I know I am several months late, but just want to respond to the other answers. All answers use simulations and/or claim the exact Fisher calculation is too computationally intensive. If you code ...
Peter Calhoun's user avatar
8 votes
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Fisher's exact test meaning of "greater" and "less"

The Fisher exact test conditions on the margins (they don't have to be fixed, necessarily; Fisher would argue that the margins are almost ancillary, though in some situations this argument might be a ...
Glen_b's user avatar
  • 285k
8 votes
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McNemar or Fisher exact test for propensity score matched data?

This is definitely an ongoing debate in the literature, but at this point the evidence points to using paired analysis to compute standard errors and p-values. Although the goal of matching is to ...
Noah's user avatar
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7 votes
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Fisher's exact test - help understanding the p-value

The table tells you a great deal. Let's begin with the first rule of data analysis: draw a picture. ...
whuber's user avatar
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7 votes
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How can p=1 in Fisher's exact test?

In any randomization test, the probability is the proportion of possible outcomes (given the data but not given the assignment to conditions) as extreme or more extreme than the actual data. If the ...
David Lane's user avatar
  • 1,394
7 votes
Accepted

What test to use when a chi-squared assumption is violated but my contingency table only has one row?

The "expected count >5" is not an assumption of the test. It's a rough rule of thumb relating to the adequacy of the chi-squared approximation to the distribution of the test statistic. An expected ...
Glen_b's user avatar
  • 285k
7 votes
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Testing the difference of proportions equal to a certain value

I don't think there is an exact test in this case, but there is an approximate test. In general, concerns about the poor approximation of the approximate test are likely to be exaggerated unless you ...
ColorStatistics's user avatar
7 votes
Accepted

Survival analysis on small sample : Chi-square test or Fisher's exact test?

If you have censoring in your times to events then a Fisher test might not properly take the censoring into account. See this page for the importance of taking censoring into account. A Fisher test, ...
EdM's user avatar
  • 94.6k
7 votes

Survival analysis on small sample : Chi-square test or Fisher's exact test?

The log-rank test does not require large samples: we can get an exact test by simply doing a permutations test on the log-rank statistic itself. For an implementation in R, here is one example. This ...
Cliff AB's user avatar
  • 21.4k
7 votes
Accepted

How can we have multiple "exact" tests?

Not really; all an exact test needs to do is accept or reject the null hypothesis based on the actual distribution of the test statistic. Consider the following two tests of whether the mean of a ...
jbowman's user avatar
  • 40k
7 votes

How can we have multiple "exact" tests?

The answer mostly comes down to definition. An exact test is one that when the assumptions it makes under $H_0$ hold, will not exceed the selected type I error rate (anywhere under the null), at any ...
Glen_b's user avatar
  • 285k
6 votes

Why do odds ratios from formula and R's fisher.test differ? Which one should one choose?

To add to the discussion here, it is useful to ask what exactly is conditioned on in this "conditional" likelihood. The Fisher test differs from other categorical analyses in that it considers all ...
AdamO's user avatar
  • 63.5k
6 votes
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Fisher's exact test vs kappa analysis

I know I answer the question two years later, but I hope some future readers may find the answer helpful. Cohen's $\kappa$ tests if there are more chance that a datum falls in the diagonal of a ...
POC's user avatar
  • 668
6 votes

Fisher's exact test or logistic regression to determine if distributions differ

A chi-squared test will be simplest and most appropriate. Fisher's exact test tests for differences conditional on fixed margins, which is almost certainly inappropriate here. Logistic regression ...
gung - Reinstate Monica's user avatar
6 votes
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Dataset for studying and teaching Fisher's exact test

(From a quick skim of the article, I'm not a fan of the analyses.) Fisher's exact test is often ill used, in my opinion (cf., here: Given the power of computers these days, is there ever a reason ...
gung - Reinstate Monica's user avatar
6 votes
Accepted

2x2 Fisher Exact Test Contingency Tables

The Fisher's Exact Test is a test of the odds ratio. If the contingency table has values enumerated by: $$\begin{array}{c|cc} & Y & \bar{Y} \\ \hline X & a & b \\ \bar{X} & c &...
AdamO's user avatar
  • 63.5k
6 votes

Fisher exact test for mutation co-occurence

The statement "I would like to test co-occurrence of germline and somatic mutation in the same gene." doesn't imply a direction for the null hypothesis of independence. So a two-sided alternative ...
dipetkov's user avatar
  • 10.4k
6 votes
Accepted

Sample size calculation in COVID-19 study

A glib answer is that they probably just plugged their numbers into a power calculator. I've attached a screenshot re-creating this power analysis in G*Power 3.1, a freely available power calculator. ...
Max S.'s user avatar
  • 1,746
6 votes

Sample size calculation in COVID-19 study

They used Fisher's exact test, which relates to sampling without replacement. But in reality this is not exactly like that, and it is more like binomial distributed data. For that case you get the ...
Sextus Empiricus's user avatar

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