topRankSummary              package:plw              R Documentation

_R_e_t_u_r_n _o_r _p_l_o_t_s _a_n_a_l_y_s_i_s _r_e_s_u_l_t _f_o_r _t_o_p _r_a_n_k_i_n_g _o_r _s_e_l_e_c_t_e_d _p_r_o_b_e _s_e_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     Returns (or plots) t-statistic and/or log2FC for each probe and
     median for each probe set. P

_U_s_a_g_e:

     plotSummaryLog2FC(model,nGenes=50,genesOfRank=1:nGenes,genes=NULL)
     plotSummaryT(model,nGenes=50,genesOfRank=1:nGenes,genes=NULL)
     topRankSummary(model,nGenes=50,genesOfRank=1:nGenes,genes=NULL)

_A_r_g_u_m_e_n_t_s:

   model: On object obtained from the function plw.

  nGenes: Gives summary for the nGenes top ranking genes

genesOfRank: Gives summary for genes ranked genesOfRank

   genes: Gives summary for specific genes.

_A_u_t_h_o_r(_s):

     Magnus Astrand

_S_e_e _A_l_s_o:

     plw

_E_x_a_m_p_l_e_s:

     # ------------------------------------------
     # Example using the result of the analysis of
     # the 6 arrays in the AffySpikeU95Subset data set

     # Loading the data
     data(AffySpikeU95Subset)

     # Defining design and contrast matrix
     group<-factor(rep(1:2,each=3))
     design<-model.matrix(~group-1)
     contrast<-matrix(c(1,-1),1,2)

     # Analyzing using plw
     model1<-plw(AffySpikeU95Subset,design=design,contrast=contrast,
                 epsilon=0.01)

     ## Selecting top genes
     topRankSummary(model1,nGenes=10)

     ## Plotting t-statistics and log2FC for top genes
     par(mfrow=c(1,2))
     plotSummaryT(model1,nGenes=20)
     plotSummaryLog2FC(model1,nGenes=20)

