RefPlus-package           package:RefPlus           R Documentation

_R_M_A _b_a_s_e_d _o_n _r_e_f_e_r_e_n_c_e _m_i_c_r_o_a_r_r_a_y_s: _R_M_A+ _a_n_d _R_M_A++ _m_e_t_h_o_d_s

_D_e_s_c_r_i_p_t_i_o_n:

     RMA+ is an extenstion of the RMA algorithm that calculates the
     probeset  intensities of a microarray using a pre-stored RMA model
     fitted on previously  obtained microarrays, e.g. reference
     microarrays. RMA++ is a further extension  based on the RMA+
     method. This package depends on the affyPLM package.

_D_e_t_a_i_l_s:


       Package:  RefPlus
       Type:     Package
       Version:  1.9.0
       Date:     2007-11-1
       License:  GPL version 2 or newer

     Use 'rma.para' to obtain the reference quantiles and the probe
     effects from a reference set, then use 'rmaplus' to calculate the
     RMA+ intensities based  on the fitted reference quantiles and
     probe effects.

_A_u_t_h_o_r(_s):

     By Kai-Ming Chang(kaiming@gmail.com)

_R_e_f_e_r_e_n_c_e_s:

     Chang,K.M., Harbron,C., South,M.C. (2006) An Exploration of 
     Extensions to the RMA Algorithm. Available with the RefPlus
     package.Avaliable with the package.

     Harbron, C, Chang, K.M., South,M.C.(2007) RefPlus : an R package
     extending the  RMA Algorithm. Bioinformatics 23, 2493-2494.

_E_x_a_m_p_l_e_s:

     if (require(affydata)) {
       ## Use Dilution in affydata package
       data(Dilution)

       ##Calculate RMA intensities using the rma function.
       Ex0<-exprs(rma(Dilution))

       ## Background correct, estimate the probe effects, and calculate the 
       ## RMA intensities using rma.para function.
       Para<-rma.para(Dilution, bg=TRUE,exp=TRUE)
       Ex1<-Para[[3]]

       ## Calculate the RMA+ intensity using rmaplus function. 
       Ex2<-rmaplus(Dilution, rmapara=Para, bg = TRUE)
     }

