Fisher's Exact Test

Upton, Graham

doi:10.2307/2982890

Cited by 362 publications

(171 citation statements)

References 11 publications

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“…We use Fisher's exact test to see if classes above a certain threshold are significantly more likely to contain architectural inconsistencies (Upton 1992). To apply this test, we sort the classes of a system into a 2×2 contingency table, depending on whether they contain architectural inconsistencies and on whether the computed metric value is below or above the percentile selected as threshold value.…”

Section: Discussionmentioning

confidence: 99%

Exploring the suitability of source code metrics for indicating architectural inconsistencies

2018

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Software architecture degradation is a phenomenon that frequently occurs during software evolution. Source code anomalies are one of the several aspects that potentially contribute to software architecture degradation. Many techniques for automating the detection of such anomalies are based on source code metrics. It is, however, unclear how accurate these techniques are in identifying the architecturally relevant anomalies in a system. The objective of this paper is to shed light on the extent to which source code metrics on their own can be used to characterize classes contributing to software architecture degradation. We performed a multi-case study on three open-source systems for each of which we gathered the intended architecture and data for 49 different source code metrics taken from seven different code quality tools. This data was analyzed to explore the links between architectural inconsistencies, as detected by applying reflexion modeling, and metric values indicating potential design problems at the implementation level. The results show that there does not seem to be a direct correlation between metrics and architectural inconsistencies. For many metrics, however, classes more problematic as indicated by their metric value seem significantly more likely to contribute to inconsistencies than less problematic classes. In particular, the fan-in, a classes' public API, and method counts seem to be suitable indicators. The fan-in metric seems to be a particularly interesting indicator, as class size does not seem to have a confounding effect on this metric. This finding may be useful for focusing code restructuring efforts on architecturally relevant metrics in case the intended architecture is not explicitly specified and to further improve architecture recovery and consistency checking tool support.

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Section: Discussionmentioning

confidence: 99%

Exploring the suitability of source code metrics for indicating architectural inconsistencies

2018

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“…A Fisher's exact test (Upton, 1992) was performed to identify the SNPs whose allele frequency differed between Meishan and European pigs (false discovery rate (FDR) < 0.01). After the test, the significant SNPs involved in all of the growth and immune genes can be regarded as the cause for the difference between Meishan and European pigs for the two traits.…”

Section: Identification Of Pleiotropic Single Nucleotide Polymorphismmentioning

confidence: 99%

Identification of pleiotropic genes and gene sets underlying growth and immunity traits: a case study on Meishan pigs

Zhang

Wang

Yang

et al. 2016

animal

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Both growth and immune capacity are important traits in animal breeding. The animal quantitative trait loci (QTL) database is a valuable resource and can be used for interpreting the genetic mechanisms that underlie growth and immune traits. However, QTL intervals often involve too many candidate genes to find the true causal genes. Therefore, the aim of this study was to provide an effective annotation pipeline that can make full use of the information of Gene Ontology terms annotation, linkage gene blocks and pathways to further identify pleiotropic genes and gene sets in the overlapping intervals of growth-related and immunity-related QTLs. In total, 55 non-redundant QTL overlapping intervals were identified, 1893 growth-related genes and 713 immunity-related genes were further classified into overlapping intervals and 405 pleiotropic genes shared by the two gene sets were determined. In addition, 19 pleiotropic gene linkage blocks and 67 pathways related to immunity and growth traits were discovered. A total of 343 growth-related genes and 144 immunity-related genes involved in pleiotropic pathways were also identified, respectively. We also sequenced and genotyped 284 individuals from Chinese Meishan pigs and European pigs and mapped the single nucleotide polymorphisms (SNPs) to the pleiotropic genes and gene sets that we identified. A total of 971 high-confidence SNPs were mapped to the pleiotropic genes and gene sets that we identified, and among them 743 SNPs were statistically significant in allele frequency between Meishan and European pigs. This study explores the relationship between growth and immunity traits from the view of QTL overlapping intervals and can be generalized to explore the relationships between other traits.

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“…F12/1 and accession Percentage rooting and mean root number were calculated from 55-65 shoots for F12/1 and Colt, and from 18 shoots for 1902. Mid-p values for comparing the proportions of shoots that rooted with and without PG were calculated using Fishers Exact Test[15].…”

mentioning

confidence: 99%

Promotion by phloroglucinol of adventitious root formation in micropropagated shoots of adult wild cherry (Prunus avium L.)

Hammatt

1994

Plant Growth Regul

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Micropropagated shoots of wild cherry (Prunus avium L.) produced roots in auxin-free medium. Phloroglucinol (PG) increased the proportion of shoots that rooted, while phloretic acid reduced this response in medium with or without PG, and cancelled the promotive effect of PG. Concentration of PG also significantly affected rooting in media with and without auxin. The proportion of shoots rooting in media containing auxin, or auxin plus PG, increased with the number of successive subcultures, but the proportion that rooted with PG alone was unaffected by the number of subcultures. Before the shoots had become responsive to auxin, 1 mM PG was more effective than auxin in inducing root formation,

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Fisher's Exact Test

Cited by 362 publications

References 11 publications

Exploring the suitability of source code metrics for indicating architectural inconsistencies

Exploring the suitability of source code metrics for indicating architectural inconsistencies

Identification of pleiotropic genes and gene sets underlying growth and immunity traits: a case study on Meishan pigs

Promotion by phloroglucinol of adventitious root formation in micropropagated shoots of adult wild cherry (Prunus avium L.)

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