# Two sample t test - equal variances not assumed - overview

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Two sample $t$ test - equal variances not assumed
One way ANOVA
Friedman test
Chi-squared test for the relationship between two categorical variables
One sample $t$ test for the mean
$z$ test for the difference between two proportions
Independent/grouping variableIndependent/grouping variableIndependent/grouping variableIndependent /column variableIndependent variableIndependent/grouping variable
One categorical with 2 independent groupsOne categorical with $I$ independent groups ($I \geqslant 2$)One within subject factor ($\geq 2$ related groups)One categorical with $I$ independent groups ($I \geqslant 2$)NoneOne categorical with 2 independent groups
Dependent variableDependent variableDependent variableDependent /row variableDependent variableDependent variable
One quantitative of interval or ratio levelOne quantitative of interval or ratio levelOne of ordinal levelOne categorical with $J$ independent groups ($J \geqslant 2$)One quantitative of interval or ratio levelOne categorical with 2 independent groups
Null hypothesisNull hypothesisNull hypothesisNull hypothesisNull hypothesisNull hypothesis
H0: $\mu_1 = \mu_2$

Here $\mu_1$ is the population mean for group 1, and $\mu_2$ is the population mean for group 2.
ANOVA $F$ test:
• H0: $\mu_1 = \mu_2 = \ldots = \mu_I$
$\mu_1$ is the population mean for group 1; $\mu_2$ is the population mean for group 2; $\mu_I$ is the population mean for group $I$
$t$ Test for contrast:
• H0: $\Psi = 0$
$\Psi$ is the population contrast, defined as $\Psi = \sum a_i\mu_i$. Here $\mu_i$ is the population mean for group $i$ and $a_i$ is the coefficient for $\mu_i$. The coefficients $a_i$ sum to 0.
$t$ Test multiple comparisons:
• H0: $\mu_g = \mu_h$
$\mu_g$ is the population mean for group $g$; $\mu_h$ is the population mean for group $h$
H0: the population scores in any of the related groups are not systematically higher or lower than the population scores in any of the other related groups

Usually the related groups are the different measurement points. Several different formulations of the null hypothesis can be found in the literature, and we do not agree with all of them. Make sure you (also) learn the one that is given in your text book or by your teacher.
H0: there is no association between the row and column variable

More precisely, if there are $I$ independent random samples of size $n_i$ from each of $I$ populations, defined by the independent variable:
• H0: the distribution of the dependent variable is the same in each of the $I$ populations
If there is one random sample of size $N$ from the total population:
• H0: the row and column variables are independent
H0: $\mu = \mu_0$

Here $\mu$ is the population mean, and $\mu_0$ is the population mean according to the null hypothesis.
H0: $\pi_1 = \pi_2$

Here $\pi_1$ is the population proportion of 'successes' for group 1, and $\pi_2$ is the population proportion of 'successes' for group 2.
Alternative hypothesisAlternative hypothesisAlternative hypothesisAlternative hypothesisAlternative hypothesisAlternative hypothesis
H1 two sided: $\mu_1 \neq \mu_2$
H1 right sided: $\mu_1 > \mu_2$
H1 left sided: $\mu_1 < \mu_2$
ANOVA $F$ test:
• H1: not all population means are equal
$t$ Test for contrast:
• H1 two sided: $\Psi \neq 0$
• H1 right sided: $\Psi > 0$
• H1 left sided: $\Psi < 0$
$t$ Test multiple comparisons:
• H1 - usually two sided: $\mu_g \neq \mu_h$
H1: the population scores in some of the related groups are systematically higher or lower than the population scores in other related groups H1: there is an association between the row and column variable

More precisely, if there are $I$ independent random samples of size $n_i$ from each of $I$ populations, defined by the independent variable:
• H1: the distribution of the dependent variable is not the same in all of the $I$ populations
If there is one random sample of size $N$ from the total population:
• H1: the row and column variables are dependent
H1 two sided: $\mu \neq \mu_0$
H1 right sided: $\mu > \mu_0$
H1 left sided: $\mu < \mu_0$
H1 two sided: $\pi_1 \neq \pi_2$
H1 right sided: $\pi_1 > \pi_2$
H1 left sided: $\pi_1 < \pi_2$
AssumptionsAssumptionsAssumptionsAssumptionsAssumptionsAssumptions
• Within each population, the scores on the dependent variable are normally distributed
• Group 1 sample is a simple random sample (SRS) from population 1, group 2 sample is an independent SRS from population 2. That is, within and between groups, observations are independent of one another
• Within each population, the scores on the dependent variable are normally distributed
• The standard deviation of the scores on the dependent variable is the same in each of the populations: $\sigma_1 = \sigma_2 = \ldots = \sigma_I$
• Group 1 sample is a simple random sample (SRS) from population 1, group 2 sample is an independent SRS from population 2, $\ldots$, group $I$ sample is an independent SRS from population $I$. That is, within and between groups, observations are independent of one another
• Sample of 'blocks' (usually the subjects) is a simple random sample from the population. That is, blocks are independent of one another
• Sample size is large enough for $X^2$ to be approximately chi-squared distributed under the null hypothesis. Rule of thumb:
• 2 $\times$ 2 table: all four expected cell counts are 5 or more
• Larger than 2 $\times$ 2 tables: average of the expected cell counts is 5 or more, smallest expected cell count is 1 or more
• There are $I$ independent simple random samples from each of $I$ populations defined by the independent variable, or there is one simple random sample from the total population
• Scores are normally distributed in the population
• Sample is a simple random sample from the population. That is, observations are independent of one another
• Sample size is large enough for $z$ to be approximately normally distributed. Rule of thumb:
• Significance test: number of successes and number of failures are each 5 or more in both sample groups
• Regular (large sample) 90%, 95%, or 99% confidence interval: number of successes and number of failures are each 10 or more in both sample groups
• Plus four 90%, 95%, or 99% confidence interval: sample sizes of both groups are 5 or more
• Group 1 sample is a simple random sample (SRS) from population 1, group 2 sample is an independent SRS from population 2. That is, within and between groups, observations are independent of one another
Test statisticTest statisticTest statisticTest statisticTest statisticTest statistic
$t = \dfrac{(\bar{y}_1 - \bar{y}_2) - 0}{\sqrt{\dfrac{s^2_1}{n_1} + \dfrac{s^2_2}{n_2}}} = \dfrac{\bar{y}_1 - \bar{y}_2}{\sqrt{\dfrac{s^2_1}{n_1} + \dfrac{s^2_2}{n_2}}}$
Here $\bar{y}_1$ is the sample mean in group 1, $\bar{y}_2$ is the sample mean in group 2, $s^2_1$ is the sample variance in group 1, $s^2_2$ is the sample variance in group 2, $n_1$ is the sample size of group 1, and $n_2$ is the sample size of group 2. The 0 represents the difference in population means according to the null hypothesis.

The denominator $\sqrt{\frac{s^2_1}{n_1} + \frac{s^2_2}{n_2}}$ is the standard error of the sampling distribution of $\bar{y}_1 - \bar{y}_2$. The $t$ value indicates how many standard errors $\bar{y}_1 - \bar{y}_2$ is removed from 0.

Note: we could just as well compute $\bar{y}_2 - \bar{y}_1$ in the numerator, but then the left sided alternative becomes $\mu_2 < \mu_1$, and the right sided alternative becomes $\mu_2 > \mu_1$.
ANOVA $F$ test:
• \begin{aligned}[t] F &= \dfrac{\sum\nolimits_{subjects} (\mbox{subject's group mean} - \mbox{overall mean})^2 / (I - 1)}{\sum\nolimits_{subjects} (\mbox{subject's score} - \mbox{its group mean})^2 / (N - I)}\\ &= \dfrac{\mbox{sum of squares between} / \mbox{degrees of freedom between}}{\mbox{sum of squares error} / \mbox{degrees of freedom error}}\\ &= \dfrac{\mbox{mean square between}}{\mbox{mean square error}} \end{aligned}
where $N$ is the total sample size, and $I$ is the number of groups.
Note: mean square between is also known as mean square model, and mean square error is also known as mean square residual or mean square within.
$t$ Test for contrast:
• $t = \dfrac{c}{s_p\sqrt{\sum \dfrac{a^2_i}{n_i}}}$
Here $c$ is the sample estimate of the population contrast $\Psi$: $c = \sum a_i\bar{y}_i$, with $\bar{y}_i$ the sample mean in group $i$. $s_p$ is the pooled standard deviation based on all the $I$ groups in the ANOVA, $a_i$ is the contrast coefficient for group $i$, and $n_i$ is the sample size of group $i$.
Note that if the contrast compares only two group means with each other, this $t$ statistic is very similar to the two sample $t$ statistic (assuming equal population standard deviations). In that case the only difference is that we now base the pooled standard deviation on all the $I$ groups, which affects the $t$ value if $I \geqslant 3$. It also affects the corresponding degrees of freedom.
$t$ Test multiple comparisons:
• $t = \dfrac{\bar{y}_g - \bar{y}_h}{s_p\sqrt{\dfrac{1}{n_g} + \dfrac{1}{n_h}}}$
$\bar{y}_g$ is the sample mean in group $g$, $\bar{y}_h$ is the sample mean in group $h$, $s_p$ is the pooled standard deviation based on all the $I$ groups in the ANOVA, $n_g$ is the sample size of group $g$, and $n_h$ is the sample size of group $h$.
Note that this $t$ statistic is very similar to the two sample $t$ statistic (assuming equal population standard deviations). The only difference is that we now base the pooled standard deviation on all the $I$ groups, which affects the $t$ value if $I \geqslant 3$. It also affects the corresponding degrees of freedom.
$Q = \dfrac{12}{N \times k(k + 1)} \sum R^2_i - 3 \times N(k + 1)$

Here $N$ is the number of 'blocks' (usually the subjects - so if you have 4 repeated measurements for 60 subjects, $N$ equals 60), $k$ is the number of related groups (usually the number of repeated measurements), and $R_i$ is the sum of ranks in group $i$.

Remember that multiplication precedes addition, so first compute $\frac{12}{N \times k(k + 1)} \times \sum R^2_i$ and then subtract $3 \times N(k + 1)$.

Note: if ties are present in the data, the formula for $Q$ is more complicated.
$X^2 = \sum{\frac{(\mbox{observed cell count} - \mbox{expected cell count})^2}{\mbox{expected cell count}}}$
Here for each cell, the expected cell count = $\dfrac{\mbox{row total} \times \mbox{column total}}{\mbox{total sample size}}$, the observed cell count is the observed sample count in that same cell, and the sum is over all $I \times J$ cells.
$t = \dfrac{\bar{y} - \mu_0}{s / \sqrt{N}}$
Here $\bar{y}$ is the sample mean, $\mu_0$ is the population mean according to the null hypothesis, $s$ is the sample standard deviation, and $N$ is the sample size.

The denominator $s / \sqrt{N}$ is the standard error of the sampling distribution of $\bar{y}$. The $t$ value indicates how many standard errors $\bar{y}$ is removed from $\mu_0$.
$z = \dfrac{p_1 - p_2}{\sqrt{p(1 - p)\Bigg(\dfrac{1}{n_1} + \dfrac{1}{n_2}\Bigg)}}$
Here $p_1$ is the sample proportion of successes in group 1: $\dfrac{X_1}{n_1}$, $p_2$ is the sample proportion of successes in group 2: $\dfrac{X_2}{n_2}$, $p$ is the total proportion of successes in the sample: $\dfrac{X_1 + X_2}{n_1 + n_2}$, $n_1$ is the sample size of group 1, and $n_2$ is the sample size of group 2.
Note: we could just as well compute $p_2 - p_1$ in the numerator, but then the left sided alternative becomes $\pi_2 < \pi_1$, and the right sided alternative becomes $\pi_2 > \pi_1.$
n.a.Pooled standard deviationn.a.n.a.n.a.n.a.
-\begin{aligned} s_p &= \sqrt{\dfrac{(n_1 - 1) \times s^2_1 + (n_2 - 1) \times s^2_2 + \ldots + (n_I - 1) \times s^2_I}{N - I}}\\ &= \sqrt{\dfrac{\sum\nolimits_{subjects} (\mbox{subject's score} - \mbox{its group mean})^2}{N - I}}\\ &= \sqrt{\dfrac{\mbox{sum of squares error}}{\mbox{degrees of freedom error}}}\\ &= \sqrt{\mbox{mean square error}} \end{aligned}

Here $s^2_i$ is the variance in group $i.$
----
Sampling distribution of $t$ if H0 were trueSampling distribution of $F$ and of $t$ if H0 were trueSampling distribution of $Q$ if H0 were trueSampling distribution of $X^2$ if H0 were trueSampling distribution of $t$ if H0 were trueSampling distribution of $z$ if H0 were true
Approximately the $t$ distribution with $k$ degrees of freedom, with $k$ equal to
$k = \dfrac{\Bigg(\dfrac{s^2_1}{n_1} + \dfrac{s^2_2}{n_2}\Bigg)^2}{\dfrac{1}{n_1 - 1} \Bigg(\dfrac{s^2_1}{n_1}\Bigg)^2 + \dfrac{1}{n_2 - 1} \Bigg(\dfrac{s^2_2}{n_2}\Bigg)^2}$
or
$k$ = the smaller of $n_1$ - 1 and $n_2$ - 1

First definition of $k$ is used by computer programs, second definition is often used for hand calculations.
Sampling distribution of $F$:
• $F$ distribution with $I - 1$ (df between, numerator) and $N - I$ (df error, denominator) degrees of freedom
Sampling distribution of $t$:
• $t$ distribution with $N - I$ degrees of freedom
If the number of blocks $N$ is large, approximately the chi-squared distribution with $k - 1$ degrees of freedom.

For small samples, the exact distribution of $Q$ should be used.
Approximately the chi-squared distribution with $(I - 1) \times (J - 1)$ degrees of freedom$t$ distribution with $N - 1$ degrees of freedomApproximately the standard normal distribution
Significant?Significant?Significant?Significant?Significant?Significant?
Two sided:
Right sided:
Left sided:
$F$ test:
• Check if $F$ observed in sample is equal to or larger than critical value $F^*$ or
• Find $p$ value corresponding to observed $F$ and check if it is equal to or smaller than $\alpha$ (e.g. .01 < $p$ < .025 when $F$ = 3.91, df between = 4, and df error = 20)

$t$ Test for contrast two sided:
$t$ Test for contrast right sided:
$t$ Test for contrast left sided:

$t$ Test multiple comparisons two sided:
• Check if $t$ observed in sample is at least as extreme as critical value $t^{**}$. Adapt $t^{**}$ according to a multiple comparison procedure (e.g., Bonferroni) or
• Find two sided $p$ value corresponding to observed $t$ and check if it is equal to or smaller than $\alpha$. Adapt the $p$ value or $\alpha$ according to a multiple comparison procedure
$t$ Test multiple comparisons right sided
• Check if $t$ observed in sample is equal to or larger than critical value $t^{**}$. Adapt $t^{**}$ according to a multiple comparison procedure (e.g., Bonferroni) or
• Find right sided $p$ value corresponding to observed $t$ and check if it is equal to or smaller than $\alpha$. Adapt the $p$ value or $\alpha$ according to a multiple comparison procedure
$t$ Test multiple comparisons left sided
• Check if $t$ observed in sample is equal to or smaller than critical value $t^{**}$. Adapt $t^{**}$ according to a multiple comparison procedure (e.g., Bonferroni) or
• Find left sided $p$ value corresponding to observed $t$ and check if it is equal to or smaller than $\alpha$. Adapt the $p$ value or $\alpha$ according to a multiple comparison procedure
If the number of blocks $N$ is large, the table with critical $X^2$ values can be used. If we denote $X^2 = Q$:
• Check if $X^2$ observed in sample is equal to or larger than critical value $X^{2*}$ or
• Find $p$ value corresponding to observed $X^2$ and check if it is equal to or smaller than $\alpha$
• Check if $X^2$ observed in sample is equal to or larger than critical value $X^{2*}$ or
• Find $p$ value corresponding to observed $X^2$ and check if it is equal to or smaller than $\alpha$
Two sided:
Right sided:
Left sided:
Two sided:
Right sided:
Left sided:
Approximate $C\%$ confidence interval for \mu_1 - \mu_2$$C\% confidence interval for \Psi, for \mu_g - \mu_h, and for \mu_in.a.n.a.C\% confidence interval for \muApproximate C\% confidence interval for \pi_1 - \pi_2 (\bar{y}_1 - \bar{y}_2) \pm t^* \times \sqrt{\dfrac{s^2_1}{n_1} + \dfrac{s^2_2}{n_2}} where the critical value t^* is the value under the t_{k} distribution with the area C / 100 between -t^* and t^* (e.g. t^* = 2.086 for a 95% confidence interval when df = 20). The confidence interval for \mu_1 - \mu_2 can also be used as significance test. Confidence interval for \Psi (contrast): • c \pm t^* \times s_p\sqrt{\sum \dfrac{a^2_i}{n_i}} where the critical value t^* is the value under the t_{N - I} distribution with the area C / 100 between -t^* and t^* (e.g. t^* = 2.086 for a 95% confidence interval when df = 20). Note that n_i is the sample size of group i, and N is the total sample size, based on all the I groups. Confidence interval for \mu_g - \mu_h (multiple comparisons): • (\bar{y}_g - \bar{y}_h) \pm t^{**} \times s_p\sqrt{\dfrac{1}{n_g} + \dfrac{1}{n_h}} where t^{**} depends upon C, degrees of freedom (N - I), and the multiple comparison procedure. If you do not want to apply a multiple comparison procedure, t^{**} = t^* = the value under the t_{N - I} distribution with the area C / 100 between -t^* and t^*. Note that n_g is the sample size of group g, n_h is the sample size of group h, and N is the total sample size, based on all the I groups. Confidence interval for single population mean \mu_i: • \bar{y}_i \pm t^* \times \dfrac{s_p}{\sqrt{n_i}} where \bar{y}_i is the sample mean in group i, n_i is the sample size of group i, and the critical value t^* is the value under the t_{N - I} distribution with the area C / 100 between -t^* and t^* (e.g. t^* = 2.086 for a 95% confidence interval when df = 20). Note that n_i is the sample size of group i, and N is the total sample size, based on all the I groups. --\bar{y} \pm t^* \times \dfrac{s}{\sqrt{N}} where the critical value t^* is the value under the t_{N-1} distribution with the area C / 100 between -t^* and t^* (e.g. t^* = 2.086 for a 95% confidence interval when df = 20). The confidence interval for \mu can also be used as significance test. Regular (large sample): • (p_1 - p_2) \pm z^* \times \sqrt{\dfrac{p_1(1 - p_1)}{n_1} + \dfrac{p_2(1 - p_2)}{n_2}} where the critical value z^* is the value under the normal curve with the area C / 100 between -z^* and z^* (e.g. z^* = 1.96 for a 95% confidence interval) With plus four method: • (p_{1.plus} - p_{2.plus}) \pm z^* \times \sqrt{\dfrac{p_{1.plus}(1 - p_{1.plus})}{n_1 + 2} + \dfrac{p_{2.plus}(1 - p_{2.plus})}{n_2 + 2}} where p_{1.plus} = \dfrac{X_1 + 1}{n_1 + 2}, p_{2.plus} = \dfrac{X_2 + 1}{n_2 + 2}, and the critical value z^* is the value under the normal curve with the area C / 100 between -z^* and z^* (e.g. z^* = 1.96 for a 95% confidence interval) n.a.Effect sizen.a.n.a.Effect sizen.a. - • Proportion variance explained \eta^2 and R^2: Proportion variance of the dependent variable y explained by the independent variable:$$ \begin{align} \eta^2 = R^2 &= \dfrac{\mbox{sum of squares between}}{\mbox{sum of squares total}} \end{align} $$Only in one way ANOVA \eta^2 = R^2. \eta^2 (and R^2) is the proportion variance explained in the sample. It is a positively biased estimate of the proportion variance explained in the population. • Proportion variance explained \omega^2: Corrects for the positive bias in \eta^2 and is equal to:$$\omega^2 = \frac{\mbox{sum of squares between} - \mbox{df between} \times \mbox{mean square error}}{\mbox{sum of squares total} + \mbox{mean square error}}$$\omega^2 is a better estimate of the explained variance in the population than \eta^2. • Cohen's d: Standardized difference between the mean in group g and in group h:$$d_{g,h} = \frac{\bar{y}_g - \bar{y}_h}{s_p}$$Cohen's d indicates how many standard deviations s_p two sample means are removed from each other. --Cohen's d: Standardized difference between the sample mean and \mu_0:$$d = \frac{\bar{y} - \mu_0}{s}$Cohen's$d$indicates how many standard deviations$s$the sample mean$\bar{y}$is removed from$\mu_0.$- Visual representationn.a.n.a.n.a.Visual representationn.a. ---- n.a.ANOVA tablen.a.n.a.n.a.n.a. - Click the link for a step by step explanation of how to compute the sum of squares. ---- n.a.Equivalent ton.a.n.a.n.a.Equivalent to -OLS regression with one categorical independent variable transformed into$I - 1$code variables: •$F$test ANOVA is equivalent to$F$test regression model •$t$test for contrast$i$is equivalent to$t$test for regression coefficient$\beta_i$(specific contrast tested depends on how the code variables are defined) ---When testing two sided: chi-squared test for the relationship between two categorical variables, where both categorical variables have 2 levels. Example contextExample contextExample contextExample contextExample contextExample context Is the average mental health score different between men and women?Is the average mental health score different between people from a low, moderate, and high economic class?Is there a difference in depression level between measurement point 1 (pre-intervention), measurement point 2 (1 week post-intervention), and measurement point 3 (6 weeks post-intervention)?Is there an association between economic class and gender? Is the distribution of economic class different between men and women?Is the average mental health score of office workers different from$\mu_0 = 50$?Is the proportion of smokers different between men and women? Use the normal approximation for the sampling distribution of the test statistic. SPSSSPSSSPSSSPSSSPSSSPSS Analyze > Compare Means > Independent-Samples T Test... • Put your dependent (quantitative) variable in the box below Test Variable(s) and your independent (grouping) variable in the box below Grouping Variable • Click on the Define Groups... button. If you can't click on it, first click on the grouping variable so its background turns yellow • Fill in the value you have used to indicate your first group in the box next to Group 1, and the value you have used to indicate your second group in the box next to Group 2 • Continue and click OK Analyze > Compare Means > One-Way ANOVA... • Put your dependent (quantitative) variable in the box below Dependent List and your independent (grouping) variable in the box below Factor or Analyze > General Linear Model > Univariate... • Put your dependent (quantitative) variable in the box below Dependent Variable and your independent (grouping) variable in the box below Fixed Factor(s) Analyze > Nonparametric Tests > Legacy Dialogs > K Related Samples... • Put the$k$variables containing the scores for the$k$related groups in the white box below Test Variables • Under Test Type, select the Friedman test Analyze > Descriptive Statistics > Crosstabs... • Put one of your two categorical variables in the box below Row(s), and the other categorical variable in the box below Column(s) • Click the Statistics... button, and click on the square in front of Chi-square • Continue and click OK Analyze > Compare Means > One-Sample T Test... • Put your variable in the box below Test Variable(s) • Fill in the value for$\mu_0$in the box next to Test Value SPSS does not have a specific option for the$z$test for the difference between two proportions. However, you can do the chi-squared test instead. The$p$value resulting from this chi-squared test is equivalent to the two sided$p$value that would have resulted from the$z$test. Go to: Analyze > Descriptive Statistics > Crosstabs... • Put your independent (grouping) variable in the box below Row(s), and your dependent variable in the box below Column(s) • Click the Statistics... button, and click on the square in front of Chi-square • Continue and click OK JamoviJamoviJamoviJamoviJamoviJamovi T-Tests > Independent Samples T-Test • Put your dependent (quantitative) variable in the box below Dependent Variables and your independent (grouping) variable in the box below Grouping Variable • Under Tests, select Welch's • Under Hypothesis, select your alternative hypothesis ANOVA > ANOVA • Put your dependent (quantitative) variable in the box below Dependent Variable and your independent (grouping) variable in the box below Fixed Factors ANOVA > Repeated Measures ANOVA - Friedman • Put the$k$variables containing the scores for the$k$related groups in the box below Measures Frequencies > Independent Samples -$\chi^2$test of association • Put one of your two categorical variables in the box below Rows, and the other categorical variable in the box below Columns T-Tests > One Sample T-Test • Put your variable in the box below Dependent Variables • Under Hypothesis, fill in the value for$\mu_0$in the box next to Test Value, and select your alternative hypothesis Jamovi does not have a specific option for the$z$test for the difference between two proportions. However, you can do the chi-squared test instead. The$p$value resulting from this chi-squared test is equivalent to the two sided$p$value that would have resulted from the$z$test. Go to: Frequencies > Independent Samples -$\chi^2\$ test of association
• Put your independent (grouping) variable in the box below Rows, and your dependent variable in the box below Columns
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