Practical 3

Exercise 1
Question 1. Compare means and medians, raw data.
Question 2. 2 Groups. Unpaired t test, Paired t test, Mann-Whitney test, Welch’s corrected test,
Wilcoxon matched pairs test

Question 3:
See image on next page.
Confidence limits: Males 51.113 – 59.387, Females 62.217 – 72.117

Question 4: Yes a statistically significant difference might be expected because the 95% confidence
limits do not overlap. This implies that the samples may have been drawn form two different
populations.

Question 5: A confidence interval is the likely range of the true value of the mean of the population
based on the mean of the sample. If the 95% level of confidence has been set, then there is a 95%
likelihood of the true mean of the population falling within that range.

Question 6: The data are unpaired.

Question 7:
The data may be assumed to have a Gaussian distribution, although this must be done with caution as
the sample sizes are relatively small. This may first be based on looking at the mean and median
values. InStat then offers you further advice under normality test at the bottom of the table, the
Normality test. InStat tests for deviations from Gaussian distribution. Since the Gaussian distribution is
also called the Normal distribution, the test is called a normality test. InStat tests for normality using
the Kolmogorov-Smirnov test. The KS statistic (which some other programs call D) quantifies the
discrepancy between the distribution of your data and an ideal Gaussian distribution - a larger value
denotes a larger discrepancy. It is not informative by itself, but is used to compute a P value.
The P value from the normality test answers this question: If you randomly sample from a Gaussian
population, what is the probability of obtaining a sample that deviates as much from a Gaussian
distribution (or more so) as this sample does. More precisely, the P value answers this question: If the
population was really Gaussian, what is the chance that a randomly selected sample of this size would
have a KS distance as large, or larger, as observed?
By looking at the distribution of a small sample of data, it is hard to tell if the values came from a
Gaussian distribution or not. Running a formal test does not make it easier. The tests simply have little
power to discriminate between Gaussian and nongaussian populations with small sample sizes. How
small? If you have fewer than five values, InStat doesn't even attempt to test for normality. But the test
doesn't really have much power to detect deviations from Gaussian distribution unless you have several
dozen values.

Question 8: A two tailed t test was selected. It is very seldom that you will ever use a one tailed test. A
one tailed test is only appropriate if you know in advance that all the subjects will respond in the same
way, ie there will always be a positive or a negative response.

Question 9: Unpaired t test. If you specified the following criteria, unpaired with equal standard
deviations and a two tailed test. If you chose a non parametric test on the basis of small sample size an
possible non Gaussian distribution then you were offered the Mann-Whitney test.

Question 10: The unpaired t test P = 0.0005 t = 4.066 with 22 degrees of freedom.

Additional information was also given to you, suggesting that you were correct in assuming that the
standard deviations were similar and that the distribution was Gaussian.

Assumption test: Are the standard deviations equal?

The t test assumes that the columns come from populations with equal SDs.
The following calculations test that assumption.
F = 1.432
The P value is 0.2808.
This test suggests that the difference between the two SDs is not significant.
Assumption test: Are the data sampled from Gaussian distributions?
The t test assumes that the data are sampled from populations that follow
Gaussian distributions. This assumption is tested using the method
Kolmogorov and Smirnov:

Group KS P Value Passed normality test?

=============== ====== ======== =======================
Male 0.1982 >0.10 Yes
Female 0.1752 >0.10 Yes

Question 11. (nmales + nfemales) – 2 = (12+12) – 2 = 22

Question 12: the F test compares the two population variances and is calculated by dividing the larger
variance by the smaller variance. Remember that the variance is the standard deviation squared.

Question 13: The P value os derived by using the F value and the degrees of freedom.

Exercise 2

Question 1: Compare means (medians)

Question 2: 2 Groups. Unpaired t test, Paired t test, Mann-Whitney test, Welch’s corrected test,
Wilcoxon matched pairs test.

Question 3: 95% confidence limits Pre: 51.113 – 59.387 and Post 62.217 – 72.117

Question 4: The data are paired. Each person’s post test marks are being compared against their pre test
marks.

Question 5: The data may be assumed to have a Gaussian distribution, although this must be done with
caution as the sample sizes are relatively small. This may first be based on looking at the mean and
median values. In Stat then offers you further advice under normality test at the bottom of the table, the
Normality test.

Question 6: A two tailed test

Question 7: Instat offered a paired and unpaired t test

Question 8: P = 0.0002

Question 9: df = n – 1 = 12 – 1 =11

Exercise 3:

Question 1: Compare means and medians. Data entry format : Average data, SD, N.

Question 2: 3 – 26 groups One way ANOVA.

Question 3: 95% confidence limits Foot: 7.816 – 11.984 AKA 52.406 – 56.394. Yes a statistically
significant difference might be expected because the 95% confidence limits do not overlap. This
implies that the samples may have been drawn form two different populations.

Question 4: All columns were chosen . Selecting all columns means that all the relevant data will be
used. Using a test would exclude some to the data and increases the chance of a type 1 error.

Question 5: One way ANOVA with post hoc testing using Bonferroni, Tukey or Student Newman
Keuls tests comparing all columns
Question 6: There are different numbers in each group. Therefore you cannot use a paired test even
though many patients had measurements taken at all sites.

Question 7: One cannot make the assumption from the data presented, as raw data are required. In
addition the assumption tests show that standard deviations are significantly different and InStat
suggests that the data be transformed or that non-parametric test be performed.

Question 8: The mean for the foot is 9.9 and the median is 0. The data are therefore negatively skewed

Question 9: The raw data are required.

Question 10: The ANOVA result shows a significant difference between sites, P<0.0001. Post hoc
testing reveals that there are differences between all the sites.

Question 11: That there are differences between all the sites

Mean
Comparison Difference q P value
================================== ========== ======= ===========
CHEST vs Foot 49.100 44.248 *** P<0.001
CHEST vs Bka 22.200 19.957 *** P<0.001
CHEST vs AKA 4.600 4.140 * P<0.05
Foot vs Bka -26.900 24.040 *** P<0.001
Foot vs AKA -44.500 39.817 *** P<0.001
Bka vs AKA -17.600 15.710 *** P<0.001

Exercise 3B

Question 1: We would not expect differences between diabetics and non diabetics at the same sites.

Question 2: One way ANOVA with post hoc testing using the Tukey Kramer test.

Question 3: All the data.

Question 4: A nonparametric test because the standard deviations are significantly different. As non
parametric tests are not available with only the summarised results, this could not be done, nor could
the data be transformed.

Question 5: No . No differences were noted between diabetics and non diabetics at the same levels.

Exercise 4

Question 1: Comparison of means (Medians), Raw data.

Question 2: Unpaired t test, Paired t test, Mann-Whitney test, Welch’s corrected test, Wilcoxon
matched pairs test.

Question 3: 95% Confidence limits Foot 1.201 – 18.599 and AKA 51.599 – 57.201

Question 4: Yes the Confidence limits suggest that these data are sampled from different populations.

Question 5: You are not given enough information to make the assumption that the data are paired.

Question 6: The foot data are skewed. The mean is 9.9 and the median is 0. The foot data do not pass
the normality test. The AKA data appear to be normally distributed.

Question 7: Non parametric test. The foot data are skewed and thus a parametric test is inappropriate.

Question 8: Mann Whitney test for unpaired and Wilcoxon matched pairs test for paired data.
Question 9: Yes. Man Whitney test returns p<0.0001.

Question 10: The level of significance is higher in this test.

Question 11: The method used in exercise 3 as all the data were used. There is also less chance of
making a type 1 error.

Exercise 5

Question 1:
Unpaired t test
P value is 0.0005, considered extremely significant.
t = 4.066 with 22 degrees of freedom.
95% confidence interval
Mean difference = 11.917 (Mean of Post test minus mean of Pre-test )
The 95% confidence interval of the difference: 5.839 to 17.995
F = 1.432
The P value is 0.2808.
Paired t test
P value is 0.0002, considered extremely significant.
t = 5.567 with 11 degrees of freedom.
95% confidence interval
Mean difference = -11.917 (Mean of paired differences)
The 95% confidence interval of the difference: -16.628 to -7.205
Assumption test: Was the pairing effective?
Correlation coefficient (r) = 0.4741
The one-tailed P value is 0.0597, considered not quite significant.
Effective pairing results in a significant correlation between the columns.
With these data, the pairing (or matching) appears not to be effective.
The unpaired test may be more appropriate.

Exercise 6

Question 1: Regression and correlation. X and Y (or 2 or more Y replicates)

Question 2: Lectures on the X axis as the independent variable and Marks on the Y axis as the
independent variable.

Question 3: y = 17.023 + 3.039x

Question 4: r = 0.9704

Question 5: R2 = 0.9417 suggests that 94% of the student marks was due to the number of lectures that
they attended.

Question 6: That there is a significant correlation between the two factors

Question 7: They are the same.

Exercise 7

Question 1: Analyse a contingency table, 2 Rows and 2 Columns

Question 2: Fishers exact test

Question 3: The two-sided P value is 0.2516, considered not significant

Question 4: No
Exercise 8

Question 1: The two-sided P value is 0.0063, considered very significant.

Question 2: No drug A is not better than Drug B. You should report on the raw data and not the
percentages.

Question 3: Yes Drug A would then be better than drug B. The P value is 0.0063