cnrma                 package:crlmm                 R Documentation

_Q_u_a_n_t_i_l_e _n_o_r_m_a_l_i_z_e_s _t_h_e _i_n_t_e_n_s_i_t_i_e_s _f_o_r _t_h_e _n_o_n_p_o_l_y_m_o_r_p_h_i_c _p_r_o_b_e
_t_o _a _H_a_p_M_a_p _r_e_f_e_r_e_n_c_e _d_i_s_t_r_i_b_u_t_i_o_n.

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

     Quantile normalizes the intensities for the nonpolymorphic probe
     to a HapMap reference distribution.

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

     cnrma(filenames, cdfName="genomewidesnp6", sns, seed = 1, verbose=FALSE)

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

filenames: filenames with complete path

 cdfName: Only 'genomewidesnp6' allowed

     sns: the sample names. If missing, the basename of the filenames
          is used.

    seed: seed for sampling the intensities to calculate skewness

 verbose: logical

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

     A list.  First element is the matrix of quantile-normalized
     intensities.  The second element is the skew.

_N_o_t_e:

     Not tested

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

     Rob Scharpf

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

             library(genomewidesnp6Crlmm)
             library(hapmapsnp6)
             path <- system.file("celFiles", package="hapmapsnp6")
             celFiles <- list.celfiles(path, full.names=TRUE)
             cnrmaResult <- cnrma(celFiles, cdfName="genomewidesnp6")

