Statnote 5: Is one set of data more variable than another?

There may be circumstances where it is necessary for microbiologists to compare variances rather than means, e,g., in analysing data from experiments to determine whether a particular treatment alters the degree of variability or testing the assumption of homogeneity of variance prior to other statistical tests. All of the tests described in this Statnote have their limitations. Bartlett’s test may be too sensitive but Levene’s and the Brown-Forsythe tests also have problems. We would recommend the use of the variance-ratio test to compare two variances and the careful application of Bartlett’s test if there are more than two groups. Considering that these tests are not particularly robust, it should be remembered that the homogeneity of variance assumption is usually the least important of those considered when carrying out an ANOVA. If there is concern about this assumption and especially if the other assumptions of the analysis are also not likely to be met, e.g., lack of normality or non additivity of treatment effects then it may be better either to transform the data or to carry out a non-parametric test on the data

Statnote 9: The one-way analysis of variance (random effects model)

There is an alternative model of the 1-way ANOVA called the 'random effects' model or ‘nested’ design in which the objective is not to test specific effects but to estimate the degree of variation of a particular measurement and to compare different sources of variation that influence the measurement in space and/or time. The most important statistics from a random effects model are the components of variance which estimate the variance associated with each of the sources of variation influencing a measurement. The nested design is particularly useful in preliminary experiments designed to estimate different sources of variation and in the planning of appropriate sampling strategies

Statnote 7: chi-square contingency tables

When the data are counts or the frequencies of particular events and can be expressed as a contingency table, then they can be analysed using the chi-square distribution. When applied to a 2 x 2 table, the test is approximate and care needs to be taken in analysing tables when the expected frequencies are small either by applying Yate’s correction or by using Fisher’s exact test. Larger contingency tables can also be analysed using this method. Note that it is a serious statistical error to use any of these tests on measurement data

Statnote 6: post-hoc ANOVA tests

If data are analysed using ANOVA, and a significant F value obtained, a more detailed analysis of the differences between the treatment means will be required. The best option is to plan specific comparisons among the treatment means before the experiment is carried out and test them using ‘contrasts’. In some circumstances, post-hoc tests may be necessary and experimenters should think carefully which of the many tests available should be used. Different tests can lead to different conclusions and careful consideration as to the appropriate test should be given in each circumstance

Statnote 8: statistical power and sample size

Statistical software is now commonly available to calculate Power (P') and sample size (N) for most experimental designs. In many circumstances, however, sample size is constrained by lack of time, cost, and in research involving human subjects, the problems of recruiting suitable individuals. In addition, the calculation of N is often based on erroneous assumptions about variability and therefore such estimates are often inaccurate. At best, we would suggest that such calculations provide only a very rough guide of how to proceed in an experiment. Nevertheless, calculation of P' is very useful especially in experiments that have failed to detect a difference which the experimenter thought was present. We would recommend that P' should always be calculated in these circumstances to determine whether the experiment was actually too small to test null hypotheses adequately

Sporulation of Clostridium difficile in aerobic conditions is significantly protracted when exposed to sodium taurocholate

Elimination of Clostridium difficile spores from the clinical setting requires stringent application of infection control procedures including the use of hard-surface disinfectants. A unique combination of sodium taurocholate together with amino acids has been reported as an alternative approach to potentially eliminating spores of C. difficile by increasing their sensitivity to common disinfectants. In this study, the efficacy of this spore germination solution was investigated to explore its effect on the sporulation process under aerobic conditions. Vegetative cells of C. difficile NCTC 11204 (Ribotype 001) and R20291 (Ribotype 027) were exposed to the germination solution comprising 6.9 mM sodium taurocholate and 50 mM of the following amino acids: histidine, glycine, arginine, aspartic acid, valine in TRIS buffer, and a control solution. Total viable counts, the rate and extent of sporulation, and percentage recovery of vegetative cells in both ribotypes were assessed by culture. At 24 hours, sporulation was protracted in ribotypes 001 and 027 and there were significantly more (p=<0.01) vegetative cells following exposure to the germination solution compared to those exposed to the control. No vegetative cells of either ribotype exposed to the control solution were detected at 24 hours. At 48 and 72 hours, vegetative cells of ribotype 027 were not detected however a significantly higher (p<0.001) percentage (43%) of viable vegetative cells of C. difficile 001 were recovered by culture. Exposing vegetative cells of C. difficile to a germination solution protracts the sporulation process in aerobic conditions. In previous studies, the application this solution to spores of C. difficile has been shown to initiate germination thus rendering them more sensitive to common disinfectants. In this investigation, the findings demonstrate that sodium taurocholate protracts the sporulation process and may provide an additional adjunct to future C. difficile infection control strategies

Statnote 4: what if the data are not normal?

When testing the difference between two groups, if previous data indicate non-normality, then either transform the data if they comprise percentages, integers or scores or use a non-parametric test. If there is uncertainty whether the data are normally distributed, then deviations from normality are likely to be small if the data are measurements to three significant figures. Unless there is clear evidence that the distribution is non-normal, it is more efficient to use the conventional t-tests. It is poor statistical practice to carry out both the parametric and non-parametric tests on a set of data and then choose the result that is most convenient to the investigator

Statnote 10: the two-way analysis of variance

The two-way design has been variously described as a matched-sample F-test, a simple within-subjects ANOVA, a one-way within-groups ANOVA, a simple correlated-groups ANOVA, and a one-factor repeated measures design! This confusion of terminology is likely to lead to problems in correctly identifying this analysis within commercially available software. The essential feature of the design is that each treatment is allocated by randomization to one experimental unit within each group or block. The block may be a plot of land, a single occasion in which the experiment was performed, or a human subject. The ‘blocking’ is designed to remove an aspect of the error variation and increase the ‘power’ of the experiment. If there is no significant source of variation associated with the ‘blocking’ then there is a disadvantage to the two-way design because there is a reduction in the DF of the error term compared with a fully randomised design thus reducing the ‘power’ of the analysis