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'.

