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| Leonardo Varuzza; Carlos A. D. E. B. Pereira. |
| This paper is about differential gene expression measured by transcript counting methods such as SAGE or MPSS. It introduces two significance tests for detection of differential expressed tags: frequentist and Bayesian. Under the frequentist view, it is proposed a test that computes the critical level as a function of each tag total frequency. Under the Bayesian view the Full Bayesian Significance Test is used considering the logistic normal distribution. The two proposed significance levels, the frequentist and the Bayesian, are compared for a data set with four libraries. The linking function between them is a Beta distribution function with mean 0.39 and standard deviation 0.30. |
| Tipo: Manuscript |
Palavras-chave: Developmental Biology; Bioinformatics. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/2002/version/1 |
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| Leonardo Varuzza; Arthur Gruber; Carlos A. B. Pereira. |
| Most of the statistical tests currently used to detect differentially expressed genes are based on asymptotic results, and perform poorly for low expression tags. Another problem is the common use of a single canonical cutoff for the significance level (p-value) of all the tags, without taking into consideration the type II error and the highly variable character of the sample size of the tags.

 This work reports the development of two significance tests for the comparison of digital expression profiles, based on frequentist and Bayesian points of view, respectively. Both tests are exact, and do not use any asymptotic considerations, thus producing more correct results for low frequency tags than the chi-square test. The... |
| Tipo: Manuscript |
Palavras-chave: Genetics & Genomics; Bioinformatics. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/2002/version/3 |
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| Leonardo Varuzza; Arthur Gruber; Carlos A. B. Pereira. |
| Most of the statistical tests currently used to detect differentially expressed genes are based on asymptotic results, and perform poorly for low expression tags. Another problem is the common use of a single canonical cutoff for the significance level (p-value) of all the tags, without taking into consideration the type II error and the highly variable character of the sample size of the tags.

 This work reports the development of two significance tests for the comparison of digital expression profiles, based on frequentist and Bayesian points of view, respectively. Both tests are exact, and do not use any asymptotic considerations, thus producing more correct results for low frequency tags than the chi-square test. The... |
| Tipo: Manuscript |
Palavras-chave: Developmental Biology; Bioinformatics. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/2002/version/2 |
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