selectSigGene           package:ArrayTools           R Documentation

_s_e_l_e_c_t _d_i_f_f_e_r_e_n_t_i_a_l_l_y _e_x_p_r_e_s_s_e_d _g_e_n_e_s _f_r_o_m _t_h_e _r_e_g_r_e_s_s_R_e_s_u_l_t _c_l_a_s_s

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

     select differentially expressed genes based on p value and/or fold
     change  from the regressResult class

_U_s_a_g_e:

     selectSigGene(object, p.value = 0.05, fc.value = 0)

_A_r_g_u_m_e_n_t_s:

  object: an 'regressResult' class

 p.value: p value

fc.value: fold change cut-off value

_V_a_l_u_e:

     an regressResult

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

     Xiwei Wu, Arthur Li

_E_x_a_m_p_l_e_s:

     data(eSetExample)
     design<- new("designMatrix", target=pData(eSetExample), covariates = "Treatment")
     contrast<- new("contrastMatrix", design.matrix = design, 
         compare1 = "Treated", compare2 = "Control")
     result<- regress(eSetExample, contrast)
     sigResult<- selectSigGene(result, fc.value=log2(2)) 

