maigesDE-class {maigesPack} | R Documentation

## maigesDE class, store results of differential gene expression analysis

### Description

This class defines a structure to store the results from differential expression analysis. This type of analysis can be done using the functions `deGenes2by2Ttest`, `deGenes2by2Wilcox` and `deGenes2by2BootT` for analysis between two biological sample types, or function `deGenesANOVA`, for analysis between more than two sample types using ANOVA models.

### Details

Objects of this class are produced by calling the functions `deGenes2by2Ttest`, `deGenes2by2Wilcox` and `deGenes2by2BootT` over an object of class `maiges` or by calling the function `deGenesANOVA` over an object of class `maigesANOVA` fitting an ANOVA model to the microarray dataset.

### Slots

`GeneInfo`:

  data frame containing the information regarding the genes from the dataset.

`SampleInfo`:

  data frame similar to the `GeneInfo` above, but containing information about the biological sample types used in the analysis.

`fold`:

  numerical matrix containing the fold values (mean difference between the sample types) when two sample types were compared. Each matrix column gives one specific test.

`stat`:

  numerical matrix giving the statistic of the tests that were done. Each column represents on test.

`p.value`:

  numerical matrix giving the p-values of the statistical tests. Again, each column represents different tests.

`factors`:

  character string giving the biological factors used in ANOVA model (when ANOVA models were used).

`test`:

  character string describing the test done.

`Date`:

  character string giving date and time that the object were created.

`V.info`:

  list containg three characters. The first one is a string containing the R version used when the object was created. The second is a char vector with base packages and the last one is another char vector with additional packages and version numbers.

### Methods

plot

  `signature(x = 'maigesDE')`: plot method for `maigesDE` class. Display volcano plots.

print

  `signature(x = 'maigesDE')`: print method for `maigesDE` class.

show

  `signature(x = 'maigesDE')`: show method for `maigesDE` class.

summary

  `signature(x = 'maigesDE')`: summary method for `maigesDE` class.

### Author(s)

Gustavo H. Esteves <gesteves@vision.ime.usp.br>

### See Also

`deGenes2by2Ttest`, `deGenes2by2Wilcox`, `deGenes2by2BootT`, `deGenesANOVA`.

[Package maigesPack version 1.44.0 Index]