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A comparison of clustering methods for biogeography with fossil datasets.

ABSTRACT: Cluster analysis is one of the most commonly used methods in palaeoecological studies, particularly in studies investigating biogeographic patterns. Although a number of different clustering methods are widely used, the approach and underlying assumptions of many of these methods are quite different. For example, methods may be hierarchical or non-hierarchical in their approaches, and may use Euclidean distance or non-Euclidean indices to cluster the data. In order to assess the effectiveness of the different clustering methods as compared to one another, a simulation was designed that could assess each method over a range of both cluster distinctiveness and sampling intensity. Additionally, a non-hierarchical, non-Euclidean, iterative clustering method implemented in the R Statistical Language is described. This method, Non-Euclidean Relational Clustering (NERC), creates distinct clusters by dividing the data set in order to maximize the average similarity within each cluster, identifying clusters in which each data point is on average more similar to those within its own group than to those in any other group. While all the methods performed well with clearly differentiated and well-sampled datasets, when data are less than ideal the linkage methods perform poorly compared to non-Euclidean based k-means and the NERC method. Based on this analysis, Unweighted Pair Group Method with Arithmetic Mean and neighbor joining methods are less reliable with incomplete datasets like those found in palaeobiological analyses, and the k-means and NERC methods should be used in their place.

SUBMITTER: Vavrek MJ

PROVIDER: S-EPMC4782735 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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A comparison of clustering methods for biogeography with fossil datasets.

Vavrek Matthew J MJ

PeerJ 20160225

Cluster analysis is one of the most commonly used methods in palaeoecological studies, particularly in studies investigating biogeographic patterns. Although a number of different clustering methods are widely used, the approach and underlying assumptions of many of these methods are quite different. For example, methods may be hierarchical or non-hierarchical in their approaches, and may use Euclidean distance or non-Euclidean indices to cluster the data. In order to assess the effectiveness of ...[more]

PMID: 26966658

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Project description:BackgroundDNA microarrays, which determine the expression levels of tens of thousands of genes from a sample, are an important research tool. However, the volume of data they produce can be an obstacle to interpretation of the results. Clustering the genes on the basis of similarity of their expression profiles can simplify the data, and potentially provides an important source of biological inference, but these methods have not been tested systematically on datasets from complex human tissues. In this paper, four clustering methods, CRC, k-means, ISA and memISA, are used upon three brain expression datasets. The results are compared on speed, gene coverage and GO enrichment. The effects of combining the clusters produced by each method are also assessed.Resultsk-means outperforms the other methods, with 100% gene coverage and GO enrichments only slightly exceeded by memISA and ISA. Those two methods produce greater GO enrichments on the datasets used, but at the cost of much lower gene coverage, fewer clusters produced, and speed. The clusters they find are largely different to those produced by k-means. Combining clusters produced by k-means and memISA or ISA leads to increased GO enrichment and number of clusters produced (compared to k-means alone), without negatively impacting gene coverage. memISA can also find potentially disease-related clusters. In two independent dorsolateral prefrontal cortex datasets, it finds three overlapping clusters that are either enriched for genes associated with schizophrenia, genes differentially expressed in schizophrenia, or both. Two of these clusters are enriched for genes of the MAP kinase pathway, suggesting a possible role for this pathway in the aetiology of schizophrenia.ConclusionConsidered alone, k-means clustering is the most effective of the four methods on typical microarray brain expression datasets. However, memISA and ISA can add extra high-quality clusters to the set produced by k-means, so combining these three methods is the method of choice.

Project description:BackgroundA Bayesian approach based on a Dirichlet process (DP) prior is useful for inferring genetic population structures because it can infer the number of populations and the assignment of individuals simultaneously. However, the properties of the DP prior method are not well understood, and therefore, the use of this method is relatively uncommon. We characterized the DP prior method to increase its practical use.ResultsFirst, we evaluated the usefulness of the sequentially-allocated merge-split (SAMS) sampler, which is a technique for improving the mixing of Markov chain Monte Carlo algorithms. Although this sampler has been implemented in a preceding program, HWLER, its effectiveness has not been investigated. We showed that this sampler was effective for population structure analysis. Implementation of this sampler was useful with regard to the accuracy of inference and computational time. Second, we examined the effect of a hyperparameter for the prior distribution of allele frequencies and showed that the specification of this parameter was important and could be resolved by considering the parameter as a variable. Third, we compared the DP prior method with other Bayesian clustering methods and showed that the DP prior method was suitable for data sets with unbalanced sample sizes among populations. In contrast, although current popular algorithms for population structure analysis, such as those implemented in STRUCTURE, were suitable for data sets with uniform sample sizes, inferences with these algorithms for unbalanced sample sizes tended to be less accurate than those with the DP prior method.ConclusionsThe clustering method based on the DP prior was found to be useful because it can infer the number of populations and simultaneously assign individuals into populations, and it is suitable for data sets with unbalanced sample sizes among populations. Here we presented a novel program, DPART, that implements the SAMS sampler and can consider the hyperparameter for the prior distribution of allele frequencies to be a variable.

Project description:Mass spectrometry is increasingly being used to discover proteins or protein profiles associated with disease. Experimental design of mass-spectrometry studies has come under close scrutiny and the importance of strict protocols for sample collection is now understood. However, the question of how best to process the large quantities of data generated is still unanswered. Main challenges for the analysis are the choice of proper pre-processing and classification methods. While these two issues have been investigated in isolation, we propose to use the classification of patient samples as a clinically relevant benchmark for the evaluation of pre-processing methods.Two in-house generated clinical SELDI-TOF MS datasets are used in this study as an example of high throughput mass-spectrometry data. We perform a systematic comparison of two commonly used pre-processing methods as implemented in Ciphergen ProteinChip Software and in the Cromwell package. With respect to reproducibility, Ciphergen and Cromwell pre-processing are largely comparable. We find that the overlap between peaks detected by either Ciphergen ProteinChip Software or Cromwell is large. This is especially the case for the more stringent peak detection settings. Moreover, similarity of the estimated intensities between matched peaks is high.We evaluate the pre-processing methods using five different classification methods. Classification is done in a double cross-validation protocol using repeated random sampling to obtain an unbiased estimate of classification accuracy. No pre-processing method significantly outperforms the other for all peak detection settings evaluated.We use classification of patient samples as a clinically relevant benchmark for the evaluation of pre-processing methods. Both pre-processing methods lead to similar classification results on an ovarian cancer and a Gaucher disease dataset. However, the settings for pre-processing parameters lead to large differences in classification accuracy and are therefore of crucial importance. We advocate the evaluation over a range of parameter settings when comparing pre-processing methods. Our analysis also demonstrates that reliable classification results can be obtained with a combination of strict sample handling and a well-defined classification protocol on clinical samples.

Dataset Information

A comparison of clustering methods for biogeography with fossil datasets.

Publications

A comparison of clustering methods for biogeography with fossil datasets.

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