maigesDE-class          package:maigesPack          R Documentation

_m_a_i_g_e_s_D_E _c_l_a_s_s, _s_t_o_r_e _r_e_s_u_l_t_s _o_f _d_i_f_f_e_r_e_n_t_i_a_l _g_e_n_e _e_x_p_r_e_s_s_i_o_n
_a_n_a_l_y_s_i_s

_D_e_s_c_r_i_p_t_i_o_n:

     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.

_D_e_t_a_i_l_s:

     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.

_S_l_o_t_s:


     '_G_e_n_e_I_n_f_o': data frame containing the information regarding the
          genes from the dataset.

     '_S_a_m_p_l_e_I_n_f_o': data frame similar to the 'GeneInfo' above, but
          containing information about the biological sample types used
          in the analysis.

     '_f_o_l_d': 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.

     '_s_t_a_t': numerical matrix giving the statistic of the tests that
          were done. Each column represents on test.

     '_p._v_a_l_u_e': numerical matrix giving the p-values of the statistical
          tests. Again, each column represents different tests.

     '_f_a_c_t_o_r_s': character string giving the biological factors used in
          ANOVA model (when ANOVA models were used).

     '_t_e_s_t': character string describing the test done.

     '_D_a_t_e': character string giving date and time that the object were
          created.

     '_V._i_n_f_o': 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.

_M_e_t_h_o_d_s:


     _p_l_o_t 'signature(x = 'maigesDE')': plot method for 'maigesDE'
          class. Display volcano plots.

     _p_r_i_n_t 'signature(x = 'maigesDE')': print method for 'maigesDE'
          class.

     _s_h_o_w 'signature(x = 'maigesDE')': show method for 'maigesDE'
          class.

     _s_u_m_m_a_r_y 'signature(x = 'maigesDE')': summary method for 'maigesDE'
          class.

_A_u_t_h_o_r(_s):

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

_S_e_e _A_l_s_o:

     'deGenes2by2Ttest', 'deGenes2by2Wilcox', 'deGenes2by2BootT',
     'deGenesANOVA'.

