basicRMA                package:oligo                R Documentation

_S_i_m_p_l_i_f_i_e_d _I_n_t_e_r_f_a_c_e _t_o _R_M_A

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

     Simple interface to RMA.

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

     basicRMA(pmMat, pnVec, normalize = TRUE, background = TRUE, bgversion = 2, destructive = FALSE, verbose = TRUE, ...)

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

   pmMat: Matrix of intensities to be processed. 

   pnVec: Probeset names. 

normalize: Logical flag: normalize? 

background: Logical flag: background adjustment? 

bgversion: Version of background correction. 

destructive: Logical flag: use destructive methods? 

 verbose: Logical flag: verbose. 

     ...: Not currently used. 

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

     Matrix.

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

     set.seed(1)
     pms <- matrix(rnorm(1000), nc=20)
     colnames(pms) <- paste("sample", 1:20, sep="")
     pns <- rep(letters[1:10], each=5)
     res <- basicRMA(pms, pns, length(unique(pns)), TRUE, TRUE)
     res[, 1:3]

