regress              package:ArrayTools              R Documentation

_R_u_n _r_e_g_r_e_s_s_i_o_n _t_o _f_i_t _g_e_n_e_w_i_s_e _l_i_n_e_a_r _m_o_d_e_l

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

     Fit genewise linear model using LIMMA package, ordinary linear
     regression, or permutation method.

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

     regress(object, contrast, method = c("limma", "regression", "permutation"), adj = "none", permute.time = 1000)

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

  object: an ExpressionSet

contrast: a contrastMatrix 

  method: choose the follwoing three options: "limma" (LIMMA), 
          "regression" (ordinary linear regression), "permutation"
          (permutation test)

     adj: adjustment method for multiple comparison test, including
          "holm",  "hochberg", "hommel", "bonferroni", "BH", "BY",
          "fdr", "none". The default  value is "none". Type
          help(p.adjust) for more detail.

permute.time: number of permutation times, only used for the
          "permutation" method

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

     an object of '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)

