selectSigGeneInt         package:ArrayTools         R Documentation

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_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 interactionResult class

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

     selectSigGeneInt(object, pGroup = 0.05, fcGroup = 0, pMain = 0.05, fcMain = 0)

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

  object: an 'interactionResult' class

  pGroup: the p value that used  to select significant genes at each
          level of the covariate

 fcGroup: the fold change value that used  to select significant genes
          at each level of the covariate

   pMain: the p values  that used to select significant genes among
          genes without any interaction effect

  fcMain: the fold change values that used to select significant genes
          among genes without any interaction effect

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

     an interactionResult

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

     Xiwei Wu, Arthur Li

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

     data(eSetExample)
     design.int<- new("designMatrix", target=pData(eSetExample), covariates = c("Treatment", "Group"),
         intIndex = c(1, 2))
     contrast.int<- new("contrastMatrix", design.matrix = design.int, interaction=TRUE)
     result.int<- regress(eSetExample, contrast.int)
     sigResult.int <- selectSigGene(result.int)
     intResult <- postInteraction(eSetExample, sigResult.int, mainVar ="Treatment",
        compare1 = "Treated", compare2 = "Control")
     sigResultInt <- selectSigGeneInt(intResult)

