logitT                  package:plw                  R Documentation

_l_o_g_i_t-_t _a_n_d _t-_t_e_s_t _b_y _r_o_w

_D_e_s_c_r_i_p_t_i_o_n:

     Functions for the logit-t test (Lemon et al. 2003) and the
     ordinary t-test computed for each row of an matrix.

_U_s_a_g_e:

     logitTTransform(pm)
     logitTStat(affy.batch,group)
     studenttTTest(x, group)

_A_r_g_u_m_e_n_t_s:

      pm: A matrix of Pm intensities

affy.batch: An AffyBatch object

   group: A group indicator vector, should have values 1 and 2 only.

       x: A matrix

_D_e_t_a_i_l_s:

     See the definition (R-code) of each function for details.

_V_a_l_u_e:

     logitTTransform returns a matrix

     logitTStat returns a vector with the logit-t statistic for each
     probe set.

     studenttTTest returns a vector with t-statistic for each row of x.

_A_u_t_h_o_r(_s):

     Magnus Astrand

_R_e_f_e_r_e_n_c_e_s:

     Lemon et al. (2003). A high performance test of differential gene
     expression for oligonucleotide arrays. Genome Biol. 2003;
     4(10):R67

_E_x_a_m_p_l_e_s:

     # ------------------------------------------
     # Example analyzing the 6 arrays in the 
     # AffySpikeU95Subset data set

     # Loading the data
     data(AffySpikeU95Subset)

     # Vector with groups assignment 
     group<-factor(rep(1:2,each=3))

     # logit-T statistic
     logitT<-logitTStat(AffySpikeU95Subset,
                        as.numeric(group))

     # Computing RMA expression index
     data.rma<-exprs(rma(AffySpikeU95Subset))

     # Ordinary t-test by row/gene
     studentT<-studenttTTest(data.rma, as.numeric(group))

     # Comparing genes ranked top-20
     logitTTop20  <- rank(-abs(logitT)) < 21
     studentTTop20<- rank(-abs(studentT)) < 21
     table(logitTTop20,studentTTop20)

