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Keywords:

  • Disease mapping;
  • False discovery rate;
  • Hierarchical Bayesian models;
  • Multiple testing;
  • Posterior probabilities

Abstract

  1. Top of page
  2. Abstract
  3. 1 Introduction
  4. 2 Motivating example
  5. 3 Statistical modeling
  6. 4 Results
  7. 5 Conclusion and discussion
  8. Acknowledgements
  9. References
  10. Supporting Information

We propose a Bayesian approach to multiple testing in disease mapping. This study was motivated by a real example regarding the mortality rate for lung cancer, males, in the Tuscan region (Italy). The data are relative to the period 1995–1999 for 287 municipalities. We develop a tri-level hierarchical Bayesian model to estimate for each area the posterior classification probability that is the posterior probability that the municipality belongs to the set of non-divergent areas. We show also the connections of our model with the false discovery rate approach. Posterior classification probabilities are used to explore areas at divergent risk from the reference while controlling for multiple testing. We consider both the Poisson-Gamma and the Besag, York and Mollié model to account for extra Poisson variability in our Bayesian formulation. Posterior inference on classification probabilities is highly dependent on the choice of the prior. We perform a sensitivity analysis and suggest how to rely on subject-specific information to derive informative a priori distributions. Hierarchical Bayesian models provide a sensible way to model classification probabilities in the context of disease mapping.


1 Introduction

  1. Top of page
  2. Abstract
  3. 1 Introduction
  4. 2 Motivating example
  5. 3 Statistical modeling
  6. 4 Results
  7. 5 Conclusion and discussion
  8. Acknowledgements
  9. References
  10. Supporting Information

Generally speaking, epidemiological surveillance consists of continuously gathering and analyzing data for changes in disease occurrence (Last, 2001). Surveillance may be based on time or space or a combination of time-space, with an active or passive approach. Disease mapping, i.e. the study of the variability of disease occurrence on space, is a cornerstone of epidemiologic surveillance. Currently, the availability of data on a small scale makes it popular to scan for abnormal disease rates potentially associated with widespread environmental exposures or to search for a localized cluster of cases in proximity of putative sources of pollution (Elliott et al., 2000). In disease mapping, a moderate to large number of area-level relative risks are considered. However, the large heterogeneity of population density among small areas leads to smaller p-values paradoxically associated with relative risk estimates closer to the null. Such inconsistency justified the development of shrinkage estimators (Clayton and Kaldor, 1987). Shrinkage estimators, as empirical Bayes or full Bayes, are now accepted as standard tools in spatial epidemiology, but they leave unresolved the multiple comparison problem.

Control of Family Wise Error Rate (FWER) that is a global control of type I error is generally pursued in the Surveillance framework (Frisén, 2003; Kulldorff, 2001). In his article of 2007, Rolka discussed the cost in sensitivity of adopting a FWER control procedure and he mentioned control of the False Discovery Rate (FDR). FDR is the rate of false positives among all rejected hypotheses and was introduced with examples in the context of clinical trials by Benjamini and Hochberg (1995). FDR has a Bayesian interpretation and it is connected to the q-value, a Bayesian alternative to the p-value (Storey, 2003).

In the disease mapping literature, posterior probability for each area having a risk higher than a predefined threshold after having specified an appropriate hierarchical Bayesian model, was suggested as a way to screen areas at higher/lower risk (Bernardinelli and Montomoli, 1992; Richardson et al., 2004). This is not sufficient to assure that the posterior inference adjusts for multiple testing. To accomplish this task, the probability model needs to include a null prior and related hyperparameters that define the prior probability mass for non-divergent areas (Scott and Berger, 2006). In the following article, we consider a two-sided alternative hypothesis and use the term divergent to denote areas at risk different from the null. This meaning of the word divergent was used by Olhssen et al. (2007).

1.1 Aim of the study

This article aims to develop a hierarchical Bayesian modeling approach to multiple testing in the context of disease mapping. The idea to use an FDR approach instead of an FWER control is based upon the fact that the erroneous rejection of the null hypothesis for some municipalities does not challenge the result of the whole descriptive analysis whose aim is to assess heterogeneity of risk in the entire study region. Therefore, the FWER control is too strict for the application's needs (Benjamini, 2009).

In the following analysis a tri-level hierarchical Bayesian model is proposed to estimate for each area the probability of belonging to the null, to be used to explore areas at divergent risk (higher or lower then the reference disease rate) while controlling for multiple testing. We took advantage of real data regarding the mortality rate due to lung cancer in males at the municipal level in the Tuscan region (Italy) during the period 1995–1999.

In Section 2, we describe the mortality data. In Section 3, we briefly introduce the problem of multiple comparisons; we then describe the proposed hierarchical Bayesian models for disease mapping and how to estimate posterior classification probabilities. The results are presented in Section 4. The conclusion and discussion follow in Section 5.

2 Motivating example

  1. Top of page
  2. Abstract
  3. 1 Introduction
  4. 2 Motivating example
  5. 3 Statistical modeling
  6. 4 Results
  7. 5 Conclusion and discussion
  8. Acknowledgements
  9. References
  10. Supporting Information

Lung cancer death certificates, for the period 1995–1999, were considered for male residents in the 287 municipalities of the Tuscan region (Italy). Data were made available by the Regional Mortality Register. The expected number of cases for each municipality was computed under indirect standardization applying a set of age-specific (18 age classes, 0–4,…, 85 or more) reference rates (Tuscany, 1971–1999) to the population of each area.

The task is to identify municipalities with a divergent risk from the reference (two-sided alternative). In fact for each i-th area out of 287, the standardized mortality ratio (observed/expected number of cases) is an estimate of the relative risk (RR), i.e. the disease risk in each area compared with the adopted standard. We have an implicit identical null hypothesis H0: RRi=1 for each area, because of the indirect standardization (Breslow and Day, 1987).

3 Statistical modeling

  1. Top of page
  2. Abstract
  3. 1 Introduction
  4. 2 Motivating example
  5. 3 Statistical modeling
  6. 4 Results
  7. 5 Conclusion and discussion
  8. Acknowledgements
  9. References
  10. Supporting Information

3.1 Multiple comparisons: general aspects

Let m be the number of hypothesis tests. The commonly controlled quantity to account for multiple testing is the FWER, and the most common method is the Bonferroni approach that is if we fix the type I error probability to α and m hypothesis tests are performed, then each test is controlled at a level of α/m (Bonferroni, 1936). This guarantees that the probability of at least one false positive is at max equal to α.

As the m null hypotheses have different implications, it can be argued that the FWER approach is too strict. Benjamini and Hochberg (1995) proposed a way to control the proportion of false rejections among the total number of rejections and introduced the FDR.

In particular, let Ii define an indicator for rejecting H0 for the i-th area, and R=∑Ii as the total number of rejections. Define also riequation image0,1equation image the indicator of the unknown true status, i.e. the indicator that the i-th area is truly not divergent from the reference.

The False Discovery Proportion (FDP) ∑(ri×Ii)/R is the fraction of false rejections over the total number of rejections (Genovese and Wasserman, 2006). Benjamini and Hochberg (1995) consider controlling the expected value of FDP, taking the expectation over repeated experiments. Let V define the number of false rejections over m hypothesis tests. The FDR is the expected value E(V/R), which can be factored as E[(V/R)∣R>0]Prob(R>0) (Benjamini and Hochberg, 1995). Storey (2003) concentrated on E[(V/R)∣R>0], a piece of the FDR, which is known as the positive FDR (pFDR).

The pFDR is defined only when at least one rejection occurred (one positive result). We cannot control pFDR because if all null hypotheses are true, any rejection is false (Storey, 2003). The pFDR can be interpreted as a posterior Bayesian probability and can be used to define the q-value, Prob(H0YYobs), Y being a test statistic and Yobs the observed value, for a generic i-th test. The q-value is the minimum pFDR that can occur rejecting the null hypothesis on the basis of the observed or more extreme values of the test statistic. The q-value is a measure that takes into account multiple testing and represents how far we are from the null hypothesis on the basis of observed data. The “frequentist” estimate of the q-value is reported in Storey (2003). It is based on the ordered p-values and it uses information on the proportion of true null hypotheses. As a referee pointed out, the frequentist estimate of the q-value reduces to the adaptive control of the Benjamini–Hochberg procedure (Benjamini and Hochberg, 2000; Benjamini et al., 2006).

Efron (2005, 2007, http://www-stat.stanford.edu/∼ckirby/brad/papers/2005LocalFDR.pdf) focused on Prob(H0Y=Yi; Y, ξ)=Prob(ri=1 ∣ Y=Yi; Y, ξ) the local FDR that is the posterior probability of the null hypothesis conditional of observed vector Y and hyperparameter vector ξ. Dealing with the local FDR differs from thresholding q-values. Generally speaking, the q-value averages over the values of the test statistic equal to or greater than Yi. As we apply tail probabilities the q-value will be less conservative than local FDR.

Efron's approach is empirical Bayes and the local FDR is calculated at some empirical value of ξ. A full Bayes approach would provide Prob(H0Y=Yi; Y)=Prob(ri=1 ∣ Y=Yi; Y), the marginal posterior probabilities, having defined a density for ξ (Müller et al., 2007).

In Section 3.2, we will briefly describe the bi-level hierarchical Bayesian models commonly used in the context of disease mapping to estimate area relative risks. In Section 3.3, we will extend these models to a tri-level Bayesian formulation to obtain fully Bayesian estimates of Prob(ri=1∣=Yi; Y), which we call posterior classification probabilities.

The reader should note that we use the term “classification probabilities” to underline the connection to the classification theory and clearly distinguish it from Prob(θi>1∣Y), which are often denoted as posterior probabilities. Barbieri and Berger (2004), referring to the problem of covariate selection, called posterior inclusion probability Prob(ri=0 ∣ Y=Yi; Y)=1 - Prob(ri=1 ∣ Y=Yi; Y).

3.2 Hierarchical models for disease mapping

Disease mapping consists of a cartographical representation of the spatial distribution of a measure of disease risk. Disease atlases in the recent years have been produced at fine spatial resolution. Risk estimates from small areas suffer from substantial extra variability and several statistical approaches have been proposed to overcome such difficulties and “stabilize” risk estimates. All these approaches rely on shrinkage estimators and among these Bayesian estimators appear to be the most appealing (Lawson et al., 1999; Elliott et al., 2000; SMMR, 2005). In this section, we describe the two most common Bayesian hierarchical models used to smooth risk estimates in disease mapping: the Poisson-Gamma model (Clayton and Kaldor, 1987), and the Besag-York-Mollié (here after known as BYM) model (Besag et al., 1991). These models will be used within our tri-level hierarchical Bayesian model in the following section.

Let area counts of disease Yi (i=1, …, 287) follow a Poisson distribution with mean Ei×θi, where Ei is the expected number of cases under indirect standardization and θi, is the relative risk. The maximum likelihood estimator of θi is called the standardized mortality ratio (SMR:equation image).

The precision of the SMR is proportional to Ei since variance (SMR)=1/Ei. For each area out of m, the p-value under the null hypothesis H0:θ=1, Prob(YYobsH0), can be easily obtained from the exact Poisson distribution.

Bayesian inference requires the specification of appropriate prior distributions on model parameters.

Clayton and Kaldor (1987), assumed a Gamma(k,ν) prior distribution for θi. The hyperparameters k and ν are assumed to be exponentially distributed. In this model, Poisson random variability is filtered out and relative risk estimates are shrunken toward the general mean.

Besag et al. (1991) specified a random effect log linear model for the relative risk log(θi)=ui+vi. The heterogeneity random term ui represents an unstructured spatial variability component assumed a priori distributed as Normal (0, λu) where λu is the precision parameter modeled as Gamma.

The clustering term vi represents the structured spatial variability component assumed to follow a priori an intrinsic conditional autoregressive (ICAR) model. In other words, denoting Si as the set of the areas adjacent to the i-th area, vivjSi is assumed distributed as Normal(equation image, λv ni) where equation image is the mean of the terms of areas adjacent to the i-th one (Besag and Kooperberg, 1995) and λv ni is the precision which is dependent on ni, the number of areas in Si. Through these two random terms the BYM model shrinks the relative risk estimates both toward the local and the general mean.

Apart from the specification of the hyperparameters, both specifications can be viewed as bi-level hierarchical models with the likelihood specified at the first level (Poisson likelihood) and the a priori distributions for the parameters of the relative risk function specified at the second.

3.3 Hierarchical Bayesian mixture model

If the goal is not estimation, but detection of areas diverging from the reference, we need to complicate the above models by introducing a third level into the hierarchy. This is equivalent to assuming a mixture model for the unknown relative risks θi.

The first level of the mixture model is again the Poisson likelihood:

  • equation image

The mixture is introduced at the second level:

  • equation image

where the logarithm of the relative risk θi is modeled as the mixture of two components: μ0i, the value of the log relative risk under the null hypothesis, and μ1i the corresponding value under the alternative. The ri indicator denotes the group membership.

Under the null we assume that all the probability mass is concentrated at one point, i.e. μ0i=0, leaving only a Poisson random variability modeled at the first level. Under the alternative extra Poisson variability, which reflects the heterogeneity of relative risk among areas, is modeled according to the two possibilities described above. The first specification is the Poisson-Gamma one, exp(μ1i) ∼ Gamma(k,ν), the second the BYM model, μ1i=ui+vi. Both the Poisson-Gamma and the convolution (BYM) models require appropriate prior distributions for the hyperparameters, as discussed in the previous section.

The third level of the hierarchy consists in the definition of the prior distribution for the indicator of the unknown true status, ri that is assumed to be Bernoulli distributed with parameter πi, which, in turn, is modeled as Beta(c,d) distribution.

The quantity of interest for each i-th area is some appropriate summary measure over the posterior distribution of πii.e. the posterior classification probability to belong to the set of the null hypothesis (Scott and Berger, 2006).

The a priori distribution for πi is assumed to be an exchangeable informative Beta(9.7,0.3) with percentiles for πi (10% : 0.91; 25% : 0.97; 50% : 0.99) and an expected value (0.97) that are sensible for a prior belief of a small percentage of divergent areas (around 3%).

3.4 Sensitivity analysis on hyperprior distribution

Posterior inference on the classification probabilities may be highly dependent on the choice of the prior. We performed a sensitivity analysis changing the parameters of the Beta(c,d) distribution. We set them to give an expected value of 0.50 (c=1,d=1) or 0.90 (c=9, d=1) for the prior belief on the null hypothesis, leaving a reasonable amount of variation (Scott and Berger, 2006, p. 2147).

All the analyses were performed using the WinBugs1.4 software (Lunn et al., 2000). For each model, we ran two independent chains and the convergence of the algorithm was performed following Gelman and Rubin (1992). We discarded the first 100 000 iterations (burn-in) and stored for estimation 50 000 iterations.

4 Results

  1. Top of page
  2. Abstract
  3. 1 Introduction
  4. 2 Motivating example
  5. 3 Statistical modeling
  6. 4 Results
  7. 5 Conclusion and discussion
  8. Acknowledgements
  9. References
  10. Supporting Information

4.1 Thresholding q-values

The map of SMR for lung cancer among males (Tuscany, Italy) in the period 1995–1999 is shown in Fig. 1(A). The map suggests the presence of high/low risk areas (SMRs range between 0 and 2.5). The reader must remember that we are testing two-sided alternative hypothesis.

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Figure 1. (A) Spatial distribution of SMRs. (B) Funnel plot of SMRs with thresholding lines (dashed: p-value<0.05; solid: q-value<0.05) (see text). Lung cancer mortality, males. Tuscany, 1995–1999.

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In Fig. 1(B), we report the funnel plot (Egger et al., 2001), which is a graph of the effect measure (SMR) against precision (Ei the inverse of SMR variance). This plot is based on the fact that the precision in estimating the risk will increase as the dimension (population) of the area increases. SMR from small areas will spread widely and the pattern will be narrow among larger areas. Under the null, the plot will resemble a symmetrical funnel centered at the reference line at an ordinate value of one. Intervals around the reference line are plotted as dashed lines corresponding to 95% percentiles of the null distribution and intervals adjusted for multiple comparison, using q-values thresholded at 5%, are plotted as solid lines. Divergent areas should lie outside the funnel lines (Jones et al., 2008).

Figure 2(B) shows the empirical distribution of two-sided p-values for each i-th area obtained from the exact Poisson distribution under the null H0: RRi=1. If no areas were to diverge, the p-value distribution would be uniform. There is an evidence of a departure from the null hypothesis. Figure 2(B) shows the quantile–quantile plot of the complementary log transformation of empirical p-values against the theoretical exponential(1) distribution under the null. The plot highlights some outlying observations.

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Figure 2. (A) Histogram of empirical p-values. (B) Quantile–Quantile plot of complementary log empirical p-values versus theoretical exponential (1). Lung cancer mortality, males. Tuscany, 1995–1999.

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Over the 287 municipalities 32 had p-values<0.05 (see the dashed funnel line in Fig. 1(B)). Applying Bonferroni's correction (with probability of type I error set at 5%) only one area is selected as divergent from the null value of one. Using Storey's q-value 11, 6, and 4 areas are selected thresholding at 20%; 10 and 5% respectively (see the solid funnel line in Fig. 1(B)). Storey's estimator of the proportion of true null gives equation image=97%.

4.2 Tri-level hierarchical Bayesian models

Figure 3 reports the maps of estimated Relative Risks by the proposed tri-level Poisson-Gamma and BYM models. The shrinking effect of the Bayesian estimators is evident when comparing it to the SMR map (Fig. 1(A)). BYM estimates are spatially smoothed and since high risk areas are clustered in the north-west part of the region, while the low risk areas are located in the south-east, the degree of shrinkage toward the general mean is less prominent. Small areas with few expected counts and extreme SMR are regressed to the mean. Since we used indirect standardization with Tuscan reference rates, the observed mean (0.97) was close to the null RR of one. Generally speaking, lung cancer risk among males showed a very strong spatial structure (see Biggeri et al., 2009).

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Figure 3. Smoothed relative risk estimates from the tri-level Poisson-Gamma and tri-level BYM models (see text). Lung cancer mortality, males. Tuscany, 1995–1999.

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Figure 4 shows the posterior inclusion probabilities (i.e. the complement to the posterior classification probabilities) from the proposed tri-level hierarchical Bayesian models. Posterior inclusion probabilities adjust for multiple comparisons. Thresholding at 90%, seven areas under the Poisson-Gamma model and nineteen areas under the BYM model were detected as divergent.

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Figure 4. Posterior inclusion probabilities Prob(ri=0 ∣ Y=Yi; Y) under the tri-level Poisson-Gamma and the tri-level BYM models (see text). Lung cancer mortality, males. Tuscany, 1995–1999.

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4.3 Model-based inclusion probabilities versus q-values

We compared the results from the tri-level hierarchical Bayesian models with those obtained thresholding q-values. In Table 1, we classified areas as divergent by cross-tabulating them with posterior classification probabilities under the tri-level hierarchical Bayesian models and by q-value. The cut-off level was set at 20%. The proportion of specific agreement ps (Fleiss et al., 2003) was 86% between tri-level Poisson-Gamma and q-value while only 43% between tri-level BYM and q-value. Disagreement between tri-level Poisson-Gamma and q-value was small and symmetrical. Instead, the spatially structured tri-level hierarchical Bayesian model “discovered” 29 divergent areas that were not detected by the q-value. Figure 5 reports the quantile-quantile plots of ordered q-values against ordered posterior classification probabilities. If the two criteria produce the same ranking, the areas will lie on the bisector. Ordering on the tri-level Poisson-Gamma posterior classification probabilities is slightly more conservative than using the q-value. The tri-level BYM behaves very differently and the selected divergent areas are spatially contiguous (Fig. 4 on the right).

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Figure 5. Quantile–Quantile plot of q-values against posterior classification probabilities (left PG: tri-level Poisson-Gamma model; right BYM: tri-level BYM model). Lung cancer mortality, males. Tuscany, 1995–1999.

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Table 1. Number of municipalities identified at altered risk by the posterior classification probabilities under the tri-level Poisson-Gamma and convolution BYM models versus q-value. The cut-off level is set to 20%. Lung cancer mortality, males. Tuscany, 1995–1999.
Poisson-Gamma posteriorclassification probabilityq-Value q-Value
 No (>0.20)Yes (≤0.20)BYM posterior classification probabilityNo (>0.20)Yes (≤0.20)
No (>0.20)2752No (>0.20)2470
Yes (≤0.20)19Yes (≤0.20)2911

4.4 Sensitivity analysis

Finally, we performed a sensitivity analysis changing the parameters of the Beta hyperprior distribution. First, we specified a Beta(1,1) for π, the probability of the null. This naïf choice, centered at 0.50, produced very unrealistic results. Indeed, as noted by Scott and Berger (2006), the researcher often has strong information about π and the information is that π is close to one. In our analysis we specified a Beta distribution on π with mean value=0.97. We alternatively specified a Beta distribution in order to give an expected value of 0.90 for the prior belief on the null hypothesis, leaving a reasonable amount of variation (first decile 0.77; first quartile 0.86; median 0.93; third quartile 0.97; last decile 0.99).

Figure 6 reports the results of the sensitivity analysis. On top, the quantile–quantile plot of posterior classification probabilities under the Beta(9.7,0.3) hyperprior versus those obtained under the uniform hyperprior and on the bottom versus those obtained under the more spread Beta(9,1) hyperprior.

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Figure 6. Sensitivity Analysis. Quantile–Quantile plot of posterior classification probabilities (left PG: tri-level Poisson-Gamma model; right BYM: tri-level BYM model) against posterior classification probabilities obtained specifying a Beta(1,1) (upper) or a Beta(9,1) (lower) hyperprior. Lung cancer mortality, males. Tuscany, 1995–1999.

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The uniform hyperprior is inappropriate, as expected. The choice of Beta(9.7,0.3) is robust to moderate change in prior belief.

5 Conclusion and discussion

  1. Top of page
  2. Abstract
  3. 1 Introduction
  4. 2 Motivating example
  5. 3 Statistical modeling
  6. 4 Results
  7. 5 Conclusion and discussion
  8. Acknowledgements
  9. References
  10. Supporting Information

As of yet, no work has been done on FDR and disease mapping. Our work on this topic started in 2006 (Catelan et al. 2006) and was motivated by an environmental epidemiological investigation on 18 high-risk areas and more than 30 disease codes. It is not surprising that until now the problem of multiple testing was not considered in disease mapping, because Bayesian approaches to smooth relative risk estimates may be misinterpreted as a solution to the problem. Bayesian estimators are superior to maximum likelihood ones when considering the whole set of estimates (earlier work was empirical Bayesian, see Clayton and Kaldor, 1987; Efron and Morris, 1973). Other epidemiological applications on long lists of relative risks appeared in Greenland and Robins (1991) and Carpenter et al. (1997).

However, estimation is a different task from testing. Indeed the inferential goals may be different. With regard to estimating relative risks, their distribution, their ranks, Sheen and Louis (1998) showed that there is no one simple best procedure. Moreover, paraphrasing Müller et al. (2007), testing multiple hypotheses requires, first that the probability model include a positive prior probability of the null for each observation, second that the model includes hyperparameters for the null prior.

A full Bayesian model that adjusts for multiple testing consists of a tri-level hierarchical Bayesian model that allows one to estimate the posterior probability to belong to the set of the null or alternative hypotheses. The advantage of using a model-based approach over a simpler frequentist one is twofold. If the model is well specified, there is a gain in power. In our application, the tri-level spatially structured hierarchical Bayesian model detected many more areas as divergent, leaving the impression of a greater power for such specification. But the reader must remember that in the real application, we have no way of telling if an area called divergent at a given threshold is in fact truly divergent. The second advantage of the Bayesian approach is that it easily allows one to perform sensitivity analysis on model assumptions (see for example Briggs et al., 2006) and, in the multiple testing framework, on prior belief of the null (Westfall et al., 1997). Bayesian modeling will also combine risk estimation and multiple testing. Connection of posterior classification probabilities and p-values is discussed in the Bayesian literature (Casella and Berger, 1987; Bayarri and Berger, 2000).

A related work to our hierarchical modeling is found in Jones et al. (2008) and Ohlssen et al. (2007). Different from us, they considered one-sided tests to avoid confusion when flagging health-care providers as good or bad. Their approach is aimed to build prediction limits around the funnel plot analogous to what is showed in Fig. 1(B). In Ohlssen et al. (2007), they developed a hierarchical Bayesian model for the null hypothesis aiming to get cross-validation predictive p-values. Interestingly, they distinguished between (i) estimating effects within a random effect model (ii) testing a simple null model using p-values and (iii) estimating posterior probability of coming from the null within a mixture model. This last point is what we addressed in the present article.

A further point regards the use of a transformation of observed/expected ratios (Grigg et al., 2009). However, we developed a full probabilistic model that did not rely on asymptotics. Some of these details can be found in a simulation study by Catelan and Biggeri (2010), where, in the usual disease mapping framework and specifying a Poisson likelihood, the assumptions underlying the Bayesian interpretation of the q-value were checked.

There is a strong sensitivity to hyperprior choice for π. We rely on subject-specific information to derive informative distributions for π, as shown in the sensitivity analysis. We conclude that the naïf choice of a uniform distribution for π is strongly expected to be in error (see Fig. 7).

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Figure 7. Hyperpriors for π (long dashed: uniform; dashed: Beta 9,1; solid: Beta 9.7, 0.3). Lung cancer mortality, males. Tuscany, 1995–1999.

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Note that we adopted the strategy to let the data itself choose π, but we specified an appropriate informative hyperprior. Storey (2003) and also Efron (2005) applied an empirical Bayesian approach to estimate π. Concerns were raised about such an approach in applications not related to omics (Jones et al. 2008). These authors noted that the amount of information about π in the data could be scant whenever the number of tests is not large enough (>one thousand). At least in the disease-mapping context where the number of tests is between one hundred and one thousand, our sensitivity analysis shows that eliciting appropriate informative hyperprior inference on π is important.

This point deserves further explanation. The Benjamini–Hochberg procedure is robust under a variety of conditions. Storey's q-value procedures have been shown to be anticonservative when the number of tests is not high, there is lack of independence, and the proportion of true null approaches one (Benjamini et al., 2006; Dudoit et al., 2008). In our application both procedures gave identical results (eleven areas thresholded at level 20%). When specifying a Beta(c,d) hyperprior with expected value of 0.97 for the probability of the null, the tri-level Bayesian hierarchical Poisson-Gamma model gave also almost equal results (ten areas threshold at level 20%). The interpretation of such results is that the implied prior belief of the null in the frequentist procedure is close to that modeled in the tri-level Bayesian hierarchical Poisson-Gamma model.

Bayesian approaches are based on model and prior assumptions. We applied two models (Poisson-Gamma and BYM), with and without spatially structured random terms, which may help the reader to appraise different data summaries with different etiological clues (see Elliott et al., 2000 and Lawson et al., 1999).

We show a Bayesian approach to multiple testing in the disease-mapping context. It cannot be viewed as an antagonist to the classical Benjamini–Hochberg procedure or its extension. On the contrary, given some prior information and assumptions, Bayesian analysis summarizes the empirical information and uncertainty. If you believe in a spatially structured model, then you would prefer the BYM assumptions. A discussion about how to run a simulation study for comparing Bayesian models was in Lawson et al. (2000). This large simulation study documented the robustness of the Poisson-Gamma and BYM models. We provided examples in which the BYM model may suffer from the same inaccuracies of other less flexible spatially structured models (Biggeri et al., 2000; 2003). Further work is necessary to extend these results to inclusion probabilities from the proposed tri-level models.

Dependency was modeled by specification of a CAR process in the alternative hypothesis by specifying a BYM model. In our application, this led to identifying a larger number of divergent areas. We should be prudent about interpreting this result. The BYM model may be closer to the true data generating model than the alternative Poisson-Gamma model, but spatially structured models may also be anticonservative even if the BYM has been proved to behave quite well in large simulation studies (Lawson et al., 2000). We do not want to stress this point, because the reader may be led to be overconfident about a given model. We prefer to show the advantage of the Bayesian approach in performing a sensitivity analysis on model assumptions and on prior belief of the null. Future developments should address FDR-adjusted inference and decision analysis.

Inference on relative risks of selected areas after viewing the data is a natural complement to investigations such as these discussed in our article. Benjamini and Yekutieli (2005) considered simultaneous and selective inference. Yekutieli (2009) presents a Bayesian framework for providing inference for selected parameters. Our model is an example of a random effect model, because the relative risk for a given area is treated as a random quantity rather than fixed. The reason is that in this particular application, area relative risk depends on the prevalence profile of risk factors and on the composition of susceptible individuals of the area population. Prevalence and susceptibility do vary and cannot be assumed as fixed because the population of a given area is a dynamic cohort. As stated by Yekutieli (2009), under a random effect model, Bayesian inference is unaffected by selection. However, simultaneous and selective inference in the disease-mapping context is an interesting topic for future developments in our work.

“Finding posterior distributions of parameters is only part of the Bayesian solution. The remainder involves decision analysis: … (this) means considering the ramifications of various decisions explicitly in terms of loss functions” (Berry and Hochberg, 1999). We did not pursue this task in the present article (for a recent contribution see for example Guindani et al., 2009). Here, as for the explorative purposes usually undertaken in disease mapping, we used posterior classification probabilities without any explicit cut-off in the same spirit as Jones et al. (2008).

Hierarchical Bayesian models provide a sensible framework to model classification probabilities in the context of disease mapping and broadly speaking, we recommend FDR-like procedures when exploring divergent areas in disease mapping.

Acknowledgements

  1. Top of page
  2. Abstract
  3. 1 Introduction
  4. 2 Motivating example
  5. 3 Statistical modeling
  6. 4 Results
  7. 5 Conclusion and discussion
  8. Acknowledgements
  9. References
  10. Supporting Information

European Union, Italian Ministry of Economic Development, Italian Ministry of Labour, Health and Social Policies Project AGIRE POR 2006-2008 Sardinia-Tuscany. Italian Ministry of Education, University and Scientific Research Project PRIN2006131039 and PRIN20072S2HT8. The Tuscany Regional Government and the Regional Mortality Registry for having provided the data.

Conflict of Interest The authors have declared no conflict of interest.

References

  1. Top of page
  2. Abstract
  3. 1 Introduction
  4. 2 Motivating example
  5. 3 Statistical modeling
  6. 4 Results
  7. 5 Conclusion and discussion
  8. Acknowledgements
  9. References
  10. Supporting Information
  • Barbieri, M. M. and Berger, J. O. (2004). Optimal predictive model selection. Annals of Statistics 32, 870897.
  • Bayarri, M. J. and Berger, J. O. (2000). P values for composite null models. Journal of the American Statistical Association 95, 11271142.
  • Benjamini, Y. (2009). Simultaneous and selective inference: current successes and future challenges. Proceedings of the 6th international Conference on Multiple Comparison Procedures. MCP2009, Tokyo.
  • Benjamini, Y. and Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society, Series B 57, 289300.
  • Benjamini, Y. and Hochberg, Y. (2000). On the adaptive control of the false discovery rate in multiple testing with independent statistics. Journal of Educational and Behavorial Statistics 25, 6083.
  • Benjamini, Y. and Yekutieli, D. (2005). False discovery rate-adjusted multiple confidence intervals for selected parameters. Journal of the American Statistical Association 100, 7181.
  • Benjamini, Y., Krieger, A. M. and Yekutieli, D. (2006). Adaptive linear step-up procedures that control the false discovery rate. Biometrika 93, 491507.
  • Bernardinelli, L. and Montomoli, C. (1992). Empirical Bayes versus fully bayesian analysis of geographical variation in disease risk. Statistics in Medicine 11, 9831007.
  • Berry, D. A. and Hochberg, Y. (1999). Bayesian perspectives on multiple comparisons. Journal of Statistical Planning and Inference 82, 215227.
  • Besag, J. and Kooperberg, G. (1995). On conditional and intrinsic autoregressions. Biometrika 82, 733746
  • Besag, J., York, J. and Mollié, A. (1991). Bayesian image restoration, with two applications in spatial statistics. Annals of the Institute of Statistical Mathematics 43, 159.
  • Biggeri, A., Catelan, D. and Dreassi, E. (2009). The epidemic of lung cancer in tuscany (Italy): a joint analysis of male and female mortality by birth cohort. Spatial and Spatio-temporal Epidemiology 1, 3140.
  • Biggeri, A., Dreassi, E., Lagazio, C. and Böhning, D. (2003). A transitional non-parametric maximum pseudo-likelihood estimator for disease mapping. Computational Statistics and Data Analysis 41, 617629.
  • Biggeri, A., Marchi, M., Lagazio, C., Martuzzi, M. and Böhning D. (2000). Non-parametric maximum likelihood estimators for disease mapping. Statistics in Medicine 19, 25392554.
  • Bonferroni, C. (1936). Teoria statistica delle classi e calcolo delle probabilità. Pubblicazioni del Regio Istituto Superiore di Scienze Economiche e Commerciali di Firenze 8, 362.
  • Breslow, N. E. and Day, N. E. (1987). Statistical Methods in Cancer Research – Volume II – The Design and Analysis of Cohort Studies. Vol. 82, IARC Scientific Publications Oxford: Oxford University Press.
  • Briggs, A., Claxton, K. and Sculpher, M. (2006). Decision Modelling for Health Economic Evaluation. Oxford University Press, Oxford.
  • Carpenter, L. M., Machonochie, N. E. S., Roman, E. and Cox, D. R. (1997). Examining associations between occupation and health by using routinely collected data. Journal of the Royal Statistical Society, Series A 160, 507521.
  • Casella, G. and Berger, R. L. (1987). Reconciling Bayesian and frequentist evidence in the one-sided testing problem. Journal of the American Statistical Association 82, 106111.
  • Catelan, D. and Biggeri, A. (2010). Multiple testing in descriptive epidemiology. GeoSpatial Health 4, 219229.
  • Catelan, D., Lagazio, C. and Biggeri, A. (2006). Spatio-temporal Epidemiological Surveillance of High Risk Industrial or Military Sites. Proceedings of the Workshop Spatial Data Methods for Environmental and Ecological Processes – section Spatio-temporal. University of Foggia, Foggia.
  • Clayton, D. and Kaldor, J. (1987). Empirical Bayes estimates of age-standardized relative risks for use in disease mapping. Biometrics 43, 671681.
  • Dudoit, S., Gilbert, H. N. and van der Laan, M. J. (2008). Resampling-based empirical Bayes multiple testing procedures for controlling generalized tail probability and expected value error rates: focus on the false discovery rate and simulation study. Biometrical Journal 50, 716744.
  • Efron, B. (2005). Local false discovery rates.
  • Efron, B. (2007). Size, power and false discovery rates. The Annals of Statistics 35, 13511377.
  • Efron, B. and Morris, C. (1973). Stein's estimation rule and its competitors – an empirical Bayes approach. Journal of the American Statistical Association 68, 117130.
  • Egger, M., Davey Smith, G. and Altman, D. G. (Eds.) (2001). Systematic Reviews in Health Care: Meta-analysis in Context (2nd edn.) BMJ Pub. Group, London.
  • Elliott, P., Wakefield, J., Best, N. and Briggs, D. (eds) (2000). Spatial Epidemiology: Methods and Applications. Oxford University Press, Oxford.
  • Fleiss, J., Levin, B. and Myunghee, C. P. (2003). Statistical Methods for Rates and Proportions. Wiley, Hoboken NJ.
  • Frisén, M. (2003). Statistical surveillance. Optimality and methods. International Statistical Review 71, 403434.
  • Gelman, A. and Rubin, D. B. (1992). Inference from iterative simulation using multiple sequences. Statistical Science 7, 457472.
  • Genovese, C. R. and Wasserman, L. (2006). Exceedance control of the false discovery proportion. Journal of the American Statistical Association 101, 14081417.
  • Greenland, S. and Robins, J. (1991). Empirical Bayes adjustments for multiple comparisons are sometimes useful. Epidemiology 2, 244251.
  • Grigg, O. A., Spiegelhalter, D. J. and Jones, H. E. (2009). Local and marginal control charts applied to methicillin resistant Staphylococcus aureus Bacteraemia reports in UK Acute National Health Service Trust. Journal of the Royal Statistical Society, Series A 172, 4966.
  • Guindani M, Müller, P. and Zhang, S. (2009). A Bayesian discovery procedure. Journal of the Royal Statistical Society, Series B 71, 905925.
  • Kulldorff, M. (2001). Prospective time-periodic geographical disease surveillance using a scan statistic. Journal of the Royal Statistical Society, Series A 164, 6172.
  • Jones, H. E., Ohlssen, D. I. and Spiegelhalter, D. J. (2008). Use of the false discovery rate when comparing multiple health care providers. Journal of Clinical Epidemiology 61, 232240
  • Last, J. M. (2001). A Dictionary of Epidemiology (5th edn.) (2008), Miquel P.. Oxford University Press, Oxford.
  • Lawson, A. B., Biggeri, A., Boehning, D., Lesaffre, E. and Viel, J-F. (1999). Disease Mapping and Risk Assessment for Public Health. Wiley, London.
  • Lawson, A. B., Biggeri, A., Boehning, D., Lesaffre, E., Viel, J.-F., Clark, A., Schlattmann, P. and Divino, F. (2000). Disease mapping models: an empirical evaluation. Statistics in Medicine 19, 22172242.
  • Lunn, D. J., Thomas, A., Best, N. and Spiegelhalter, D. (2000). WinBUGS – a Bayesian modelling framework: concepts, structure, and extensibility. Statistics and Computing 10, 325337.
  • Müller, P., Parmigiani, G. and Rice, K. (2007). FDR and Bayesian Multiple Comparisons Rules. In: Bernardo, J.M. et al. (Eds.). Bayesian Statistics, Vol. 8. Proceedings of the Valencia/ISBA 8th World Meeting on Bayesian Statistics. Oxford University Press, Oxford.
  • Ohlssen, D. I., Sharples, L. D. and Spiegelhalter, D. J. (2007). A hierarchical modelling framework for identifying unusual performance in health care providers. Journal of the Royal Statistical Society, Series A 170, 865890.
  • Richardson, S., Thomson, A., Best, N. and Elliott, P. (2004). Interpreting posterior relative risk estimates in disease-mapping studies. Environmental Health Perspectives 112, 10161025.
  • Rolka, H., Burkom, H., Cooper, G., Kulldorff, M., Madigan, D. and Wong, W. K. (2007). Issues in applied statistics for public health bioterrorism surveillance using multiple data streams: research need. Statistics in Medicine 26, 18341856.
  • Scott, J. G. and Berger, J. O. (2006). An exploration of aspects of Bayesian multiple testing. Journal of Statistical Planning and Inference 136, 21442162.
  • Shen, W. and Louis, T. A. (1998). Triple-goal estimates in two-stage hierarchical models. Journal of the Royal Statistical Society, Series B 60, 455471.
  • SMMR (2005). Special issue on disease mapping. Statistacal Methods in Medical Research 14.
  • Storey, J. D. (2003). The positive false discovery rate: a Bayesian Interpretation and the Q-value. Annals of Statistics 31, 20132035.
  • Yekutieli, D. (2009). Adjusted Bayesian inference for Selected Parameters. Technical Report arXiv-0801.0499v4, University of Tel Aviv.
  • Westfall, P. H., Johnson, W. O. and Utts, J. M. (1997). A Bayesian perspective on the Bonferroni adjustment. Biometrika 84, 419427.

Supporting Information

  1. Top of page
  2. Abstract
  3. 1 Introduction
  4. 2 Motivating example
  5. 3 Statistical modeling
  6. 4 Results
  7. 5 Conclusion and discussion
  8. Acknowledgements
  9. References
  10. Supporting Information

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