norm1c                 package:nudge                 R Documentation

_F_u_n_c_t_i_o_n _f_o_r _n_o_r_m_a_l_i_z_i_n_g _t_h_e _m_e_a_n _o_f _a_v_e_r_a_g_e-_a_c_r_o_s_s-_r_e_p_l_i_c_a_t_e_s _l_o_g _r_a_t_i_o_s

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

     This is essentially the same as the lowess normalization suggested
     in the paper "Statistical methods for identifying differentially
     expressed genes in replicated cDNA microarrays" by Dudoit et al
     (2002), except the loess function and average-across-replicates
     log ratios are used and the recommended span is between 0.6 and
     0.8. The normalization is done for each gene by subtracting from
     its average-across-replicates log ratio the loess estimated mean
     for average-across-replicates log ratio based on the loess
     regression of average-across-replicates log ratios on
     average-across-replicates log total intensities.

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

     norm1c(logratio, logintensity, span = 0.6)

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

logratio: A multiple-column matrix of replicates of log (base 2) ratios
          of gene expressions in two samples.

logintensity: A multiple-column matrix of replicates of log (base 2)
          total intensities (defined as the product) of gene
          expressions in two samples.

    span: Proportion of data used to fit the loess regression of the
          average-across-replicates log ratios on the
          average-across-replicates log total intensities

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

     A vector of mean normalized average-across-replicates log ratios.

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

     N. Dean and A. E. Raftery

_R_e_f_e_r_e_n_c_e_s:

     N. Dean and A. E. Raftery (2005). Normal uniform mixture
     differential gene expression detection for cDNA microarrays.  BMC
     Bioinformatics. 6, 173-186. 

     <URL: http://www.biomedcentral.com/1471-2105/6/173>

     S. Dudoit, Y. H. Yang, M. Callow and T. Speed (2002). Statistical
     methods for identifying differentially expressed genes in
     replicated cDNA microarray experiments. Stat. Sin. 12, 111-139.

_S_e_e _A_l_s_o:

     'norm1d','norm1a','norm1b','norm2c','norm2d'

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

     data(hiv)
     lR<-log(hiv[,1:4],2)-log(hiv[,5:8],2)
     lI<-log(hiv[,1:4],2)+log(hiv[,5:8],2)

     lRnorm<-norm1c(lR,lI)

